diff --git a/CHANGELOG.md b/CHANGELOG.md index c48e9579..09a7b9d5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ * Update README (PR #177). +* Add authors to package config and update author information (PR #180). + # biobox 0.3.1 ## NEW FUNCTIONALITY diff --git a/_viash.yaml b/_viash.yaml index 6bfe2f08..d77adad0 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -20,5 +20,31 @@ links: viash_version: 0.9.4 +authors: + - __merge__: /src/_authors/robrecht_cannoodt.yaml + roles: [ author, maintainer ] + - __merge__: /src/_authors/angela_o_pisco.yaml + roles: [ author ] + - __merge__: /src/_authors/dorien_roosen.yaml + roles: [ author ] + - __merge__: /src/_authors/dries_schaumont.yaml + roles: [ author ] + - __merge__: /src/_authors/emma_rousseau.yaml + roles: [ author ] + - __merge__: /src/_authors/jakub_majercik.yaml + roles: [ author ] + - __merge__: /src/_authors/kai_waldrant.yaml + roles: [ author ] + - __merge__: /src/_authors/leila_paquay.yaml + roles: [ author ] + - __merge__: /src/_authors/sai_nirmayi_yasa.yaml + roles: [ author ] + - __merge__: /src/_authors/theodoro_gasperin.yaml + roles: [ author ] + - __merge__: /src/_authors/toni_verbeiren.yaml + roles: [ author ] + - __merge__: /src/_authors/weiwei_schultz.yaml + roles: [ author ] + config_mods: | .requirements.commands := ['ps'] diff --git a/src/_authors/emma_rousseau.yaml b/src/_authors/emma_rousseau.yaml index 1a9ac456..cbd15330 100644 --- a/src/_authors/emma_rousseau.yaml +++ b/src/_authors/emma_rousseau.yaml @@ -1,10 +1,6 @@ name: Emma Rousseau info: links: - email: emma@data-intuitive.com github: emmarousseau linkedin: emmarousseau1 - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Bioinformatician + diff --git a/src/_authors/kai_waldrant.yaml b/src/_authors/kai_waldrant.yaml index a132c528..ff3489bb 100644 --- a/src/_authors/kai_waldrant.yaml +++ b/src/_authors/kai_waldrant.yaml @@ -1,14 +1,7 @@ name: Kai Waldrant info: links: - email: kai@data-intuitive.com github: KaiWaldrant orcid: "0009-0003-8555-1361" linkedin: kaiwaldrant - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Bioinformatician - - name: Open Problems - href: https://openproblems.bio - role: Contributor + diff --git a/src/_authors/leila_paquay.yaml b/src/_authors/leila_paquay.yaml index 21aa532d..37b3bc04 100644 --- a/src/_authors/leila_paquay.yaml +++ b/src/_authors/leila_paquay.yaml @@ -1,10 +1,6 @@ name: Leïla Paquay info: links: - email: leila@data-intuitive.com github: Leila011 linkedin: leilapaquay - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Software Developer + diff --git a/src/_authors/sai_nirmayi_yasa.yaml b/src/_authors/sai_nirmayi_yasa.yaml index 9f560c58..2d03610f 100644 --- a/src/_authors/sai_nirmayi_yasa.yaml +++ b/src/_authors/sai_nirmayi_yasa.yaml @@ -1,10 +1,5 @@ name: Sai Nirmayi Yasa info: links: - email: nirmayi@data-intuitive.com github: sainirmayi linkedin: sai-nirmayi-yasa - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Junior Bioinformatics Researcher diff --git a/src/_authors/theodoro_gasperin.yaml b/src/_authors/theodoro_gasperin.yaml index 47af96a9..4df0d04c 100644 --- a/src/_authors/theodoro_gasperin.yaml +++ b/src/_authors/theodoro_gasperin.yaml @@ -4,7 +4,4 @@ info: email: theodorogtc@gmail.com github: tgaspe linkedin: theodoro-gasperin-terra-camargo - organizations: - - name: Data Intuitive - href: https://www.data-intuitive.com - role: Bioinformatician + diff --git a/src/_authors/weiwei_schultz.yaml b/src/_authors/weiwei_schultz.yaml index e4945078..8a480129 100644 --- a/src/_authors/weiwei_schultz.yaml +++ b/src/_authors/weiwei_schultz.yaml @@ -1,5 +1,7 @@ name: Weiwei Schultz info: + links: + linkedin: weiwei-schultz organizations: - name: Janssen R&D US role: Associate Director Data Sciences diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index 7182133e..473c1f06 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -238,9 +233,9 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -265,6 +260,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index e098a083..68254e1d 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml index 9b0e344d..7c0555fc 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -228,9 +223,9 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -255,6 +250,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index f6e26f14..b65addc3 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml index 6b2f87d6..f7038aed 100644 --- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -233,9 +228,9 @@ build_info: output: "target/executable/agat/agat_convert_genscan2gff" executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -260,6 +255,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff index 7a9544bc..55c862a2 100755 --- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff +++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml index 5d8882fb..744fd463 100644 --- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -189,9 +184,9 @@ build_info: output: "target/executable/agat/agat_convert_mfannot2gff" executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -216,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff index f47c874f..d85c79ef 100755 --- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff +++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_mfannot2gff" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index a03ecb48..4c6057a3 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -231,9 +226,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -258,6 +253,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf index 5bf92669..4419e686 100755 --- a/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf +++ b/target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 434c6fc3..cbf8d904 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -191,9 +186,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -218,6 +213,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv index 5f640747..fd72885b 100755 --- a/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv +++ b/target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 1f55ec5c..e401d305 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -198,9 +193,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -225,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf index 63c273ad..6f358888 100755 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml index ea879fe1..727513e6 100644 --- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -189,9 +184,9 @@ build_info: output: "target/executable/agat/agat_sp_add_introns" executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -216,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns index 7db1c0fc..ed049212 100755 --- a/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns +++ b/target/executable/agat/agat_sp_add_introns/agat_sp_add_introns @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_add_introns" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index fdd0f7ef..c1076e1d 100644 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -239,9 +234,9 @@ build_info: output: "target/executable/agat/agat_sp_filter_feature_from_kill_list" executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -266,6 +261,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list index 385f4be5..3b157d26 100755 --- a/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list +++ b/target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_filter_feature_from_kill_list" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml index 79ebc264..695ad06d 100644 --- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -187,9 +182,9 @@ build_info: output: "target/executable/agat/agat_sp_merge_annotations" executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -214,6 +209,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations index d70382e6..6499f8b3 100755 --- a/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations +++ b/target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_merge_annotations" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml index 596194b4..105ec3d7 100644 --- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -234,9 +229,9 @@ build_info: output: "target/executable/agat/agat_sp_statistics" executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -261,6 +256,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sp_statistics/agat_sp_statistics b/target/executable/agat/agat_sp_statistics/agat_sp_statistics index fc8ae8c1..d017f39b 100755 --- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics +++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics @@ -452,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml index efc6857d..5af3daa6 100644 --- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -230,9 +225,9 @@ build_info: output: "target/executable/agat/agat_sq_stat_basic" executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -257,6 +252,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic index ca818131..ff8fb03b 100755 --- a/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic +++ b/target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic @@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t LABEL org.opencontainers.image.authors="Leïla Paquay" LABEL org.opencontainers.image.description="Companion container for running component agat agat_sq_stat_basic" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index 131ce735..f9d15cb2 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -709,9 +709,9 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -736,6 +736,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 7e54a419..e3a058d1 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -452,9 +452,9 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' > LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component arriba" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bases2fastq/.config.vsh.yaml b/target/executable/bases2fastq/.config.vsh.yaml index 11ed497f..db4e858b 100644 --- a/target/executable/bases2fastq/.config.vsh.yaml +++ b/target/executable/bases2fastq/.config.vsh.yaml @@ -397,9 +397,9 @@ build_info: output: "target/executable/bases2fastq" executable: "target/executable/bases2fastq/bases2fastq" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -424,6 +424,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bases2fastq/bases2fastq b/target/executable/bases2fastq/bases2fastq index dbf1885c..1cfbdcd4 100755 --- a/target/executable/bases2fastq/bases2fastq +++ b/target/executable/bases2fastq/bases2fastq @@ -456,9 +456,9 @@ RUN echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bases2fastq" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml index 1d1c3631..3b665ec0 100644 --- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -371,9 +371,9 @@ build_info: output: "target/executable/bbmap/bbmap_bbsplit" executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -398,6 +398,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit index 1f73ea17..3ffd0617 100755 --- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit @@ -454,9 +454,9 @@ cp -r bbmap/* /usr/local/bin RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml index 5c17a2f9..9ea23125 100644 --- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -472,9 +468,9 @@ build_info: output: "target/executable/bcftools/bcftools_annotate" executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -499,6 +495,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate index de163734..eb88a419 100755 --- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml index 7a13cf78..83e575bb 100644 --- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -338,9 +334,9 @@ build_info: output: "target/executable/bcftools/bcftools_concat" executable: "target/executable/bcftools/bcftools_concat/bcftools_concat" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -365,6 +361,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat index 036ba09f..ddbdfca9 100755 --- a/target/executable/bcftools/bcftools_concat/bcftools_concat +++ b/target/executable/bcftools/bcftools_concat/bcftools_concat @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml index cf3b061f..246b6aca 100644 --- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -419,9 +415,9 @@ build_info: output: "target/executable/bcftools/bcftools_norm" executable: "target/executable/bcftools/bcftools_norm/bcftools_norm" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -446,6 +442,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm index a3bd4d14..46230775 100755 --- a/target/executable/bcftools/bcftools_norm/bcftools_norm +++ b/target/executable/bcftools/bcftools_norm/bcftools_norm @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml index 1706d370..f3bb8db9 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -188,9 +184,9 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -215,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index fd40007f..50aa99c2 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml index 25b3d063..f20ea4df 100644 --- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -461,9 +457,9 @@ build_info: output: "target/executable/bcftools/bcftools_stats" executable: "target/executable/bcftools/bcftools_stats/bcftools_stats" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -488,6 +484,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 12c4be97..22c15cd8 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcl_convert/.config.vsh.yaml b/target/executable/bcl_convert/.config.vsh.yaml index 07231309..7b947e0b 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -431,9 +431,9 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -458,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index bb64d493..88912831 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -462,9 +462,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/ LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component bcl_convert" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index 5b8f058f..6a7cdced 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -23,6 +23,8 @@ authors: roles: - "contributor" info: + links: + linkedin: "weiwei-schultz" organizations: - name: "Janssen R&D US" role: "Associate Director Data Sciences" @@ -277,9 +279,9 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -304,6 +306,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference index 6ece74fb..6b1ad889 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference +++ b/target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index 433c7a5d..47ccb988 100644 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -23,6 +23,8 @@ authors: roles: - "contributor" info: + links: + linkedin: "weiwei-schultz" organizations: - name: "Janssen R&D US" role: "Associate Director Data Sciences" @@ -1118,9 +1120,9 @@ build_info: output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1145,6 +1147,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis index 3aee8864..abb0feb6 100755 --- a/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis +++ b/target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis @@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml index 86b910ca..25fd90ab 100644 --- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -238,9 +234,9 @@ build_info: output: "target/executable/bedtools/bedtools_bamtobed" executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -265,6 +261,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed index b068ed50..9d8262a0 100755 --- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed +++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml index f84b1258..61c5710a 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -190,9 +186,9 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -217,6 +213,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 59037466..23d37569 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 8198098d..28481a5b 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -179,9 +175,9 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -206,6 +202,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index 24d2296f..5d6724be 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml index 530c1dbc..31217ff4 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -217,9 +213,9 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -244,6 +240,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index 381a119f..ca9c7766 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index 9ef4d472..792fa65f 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -340,9 +336,9 @@ build_info: output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -367,6 +363,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index 142c896c..009c790d 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml index 1a8df2de..6bf64a9d 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -262,6 +262,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index ba9b170a..e87141e5 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index b38749d6..62b289cf 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -276,9 +272,9 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -303,6 +299,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 0541d128..33e92494 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml index 0e2f28a5..fe2178cf 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -413,9 +409,9 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -440,6 +436,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index 73c87b80..1c8f923d 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index 3a284802..adaedfeb 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -213,9 +209,9 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -240,6 +236,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 5ff7d127..8d4ffa53 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml index 49d4a042..99bfcca1 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -282,9 +278,9 @@ build_info: output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -309,6 +305,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index e3d7e8bc..f416cc85 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:27Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index 7862e120..65b6fade 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -225,9 +221,9 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -252,6 +248,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index c9350d28..df1d5f11 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort" -LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_download_datasets/.config.vsh.yaml b/target/executable/busco/busco_download_datasets/.config.vsh.yaml index de519ccb..0e5e1fa0 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -161,9 +161,9 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -188,6 +188,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index c3097f60..c5c5d788 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_list_datasets/.config.vsh.yaml b/target/executable/busco/busco_list_datasets/.config.vsh.yaml index f9e009ce..a17dc310 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -175,6 +175,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 2757995d..a7401622 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/busco/busco_run/.config.vsh.yaml b/target/executable/busco/busco_run/.config.vsh.yaml index 09f533d7..ab96d858 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -426,9 +426,9 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -453,6 +453,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 620e8de6..ca55e5a5 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component busco busco_run" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cellranger/cellranger_count/.config.vsh.yaml b/target/executable/cellranger/cellranger_count/.config.vsh.yaml index da5205a7..f81e43d6 100644 --- a/target/executable/cellranger/cellranger_count/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_count/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "author" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - name: "Robrecht Cannoodt" roles: - "author" @@ -378,9 +373,9 @@ build_info: output: "target/executable/cellranger/cellranger_count" executable: "target/executable/cellranger/cellranger_count/cellranger_count" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -405,6 +400,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cellranger/cellranger_count/cellranger_count b/target/executable/cellranger/cellranger_count/cellranger_count index ec08d79d..07af99e9 100755 --- a/target/executable/cellranger/cellranger_count/cellranger_count +++ b/target/executable/cellranger/cellranger_count/cellranger_count @@ -456,9 +456,9 @@ RUN cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_count" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml index 880fdda5..72724ca5 100644 --- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "author" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Arguments" arguments: @@ -198,9 +193,9 @@ build_info: output: "target/executable/cellranger/cellranger_mkref" executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -225,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cellranger/cellranger_mkref/cellranger_mkref b/target/executable/cellranger/cellranger_mkref/cellranger_mkref index c522f183..53af926c 100755 --- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref +++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref @@ -454,9 +454,9 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 219fb9ea..0523babb 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -743,9 +743,9 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -770,6 +770,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index d9dbcfc6..3f7939c1 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -455,9 +455,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component cutadapt" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:18Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index 2d9dd381..31a086a9 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -320,9 +320,9 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -347,6 +347,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index 1119e37f..8b319196 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -464,9 +464,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index b95151a0..edec142f 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1086,9 +1086,9 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1113,6 +1113,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index 6c968c1a..37bf8a1f 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -452,9 +452,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component fastp" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:18Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 1a5d8d56..b17632c6 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -343,9 +339,9 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -370,6 +366,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 80b82298..a9c4b1f0 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -452,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_ LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index dfa08618..61d20964 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -648,9 +643,9 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -675,6 +670,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 69c2aa8b..22c46deb 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -452,9 +452,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component featurecounts" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 73f9e93d..2d7d8e6b 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -193,9 +193,9 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -220,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index c160d56a..c30f9a61 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -453,9 +453,9 @@ mv target/release/fq /usr/local/bin/ && \ cd / && rm -rf /fq LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index a2a4e7c3..1a0e1664 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -688,9 +683,9 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -715,6 +710,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index 343c3a40..15fe184c 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -452,9 +452,9 @@ RUN echo "gffread: \"$(gffread --version 2>&1)\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component gffread" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 55c604d3..7b773b52 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -221,9 +221,9 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -248,6 +248,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index 3d89396a..a312413e 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -452,9 +452,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 26f377e8..efc17df6 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -249,9 +249,9 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -276,6 +276,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index fd1c8b80..99c41d9f 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -454,9 +454,9 @@ mv kallisto/kallisto /usr/local/bin/ RUN echo "kallisto: $(kallisto version | sed 's/kallisto, version //')" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_call/.config.vsh.yaml b/target/executable/lofreq/lofreq_call/.config.vsh.yaml index 7de2b2d3..b9419d78 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -8,17 +8,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -510,9 +502,9 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -537,6 +529,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index bbab53df..a7280e8c 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_call" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml index 2f882934..5fe1f81b 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -8,17 +8,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -218,9 +210,9 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -245,6 +237,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index 093fdc72..fb3e7600 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -453,9 +453,9 @@ echo "lofreq: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component lofreq lofreq_indelqual" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 10b404ba..430fa82b 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -459,9 +459,9 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -486,6 +486,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index 4310712e..10bc30c9 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -452,9 +452,9 @@ RUN multiqc --version | sed 's/multiqc, version\s\(.*\)/multiqc: "\1"/' > /var/s LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component multiqc" -LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/nanoplot/.config.vsh.yaml b/target/executable/nanoplot/.config.vsh.yaml index 6e0d4ca9..12c1124e 100644 --- a/target/executable/nanoplot/.config.vsh.yaml +++ b/target/executable/nanoplot/.config.vsh.yaml @@ -495,9 +495,9 @@ build_info: output: "target/executable/nanoplot" executable: "target/executable/nanoplot/nanoplot" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -522,6 +522,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/nanoplot/nanoplot b/target/executable/nanoplot/nanoplot index 861ed889..90fb224f 100755 --- a/target/executable/nanoplot/nanoplot +++ b/target/executable/nanoplot/nanoplot @@ -449,9 +449,9 @@ RUN version=$(NanoPlot --version) && \ echo "$version" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component nanoplot" -LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index a7d9d9bd..8965370b 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -7,17 +7,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -401,9 +393,9 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -428,6 +420,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 97a62d5e..f3b79875 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -453,9 +453,9 @@ echo "pear: $version" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component pear" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml index a027cc69..301f730c 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -267,9 +267,9 @@ build_info: output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -294,6 +294,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index 01956259..a38fb7f2 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -452,9 +452,9 @@ RUN echo QualiMap: $(qualimap 2>&1 | grep QualiMap | sed 's/^.*QualiMap//') > /v LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component qualimap qualimap_rnaseq" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index 75c8010c..7481ffc2 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -855,9 +855,9 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -882,6 +882,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index c177f690..46b24767 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -470,9 +470,9 @@ echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml index c0d51a8e..0832a925 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -419,9 +414,9 @@ build_info: output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -446,6 +441,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index 98b5c018..92e73574 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -494,9 +494,9 @@ echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference" -LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 053a169e..1159b0cf 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -178,9 +173,9 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -205,6 +200,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 7400a0cd..174bfa20 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -455,9 +455,9 @@ RUN echo "RSeQC bam_stat.py: $(bam_stat.py --version | cut -d' ' -f2-)" > /var/s LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 9092f7ff..1c645133 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -204,9 +199,9 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -231,6 +226,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 397f8995..3b6dc8f7 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -455,9 +455,9 @@ RUN echo "RSeQC - infer_experiment.py: $(infer_experiment.py --version | cut -d' LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml index fba15eb4..7a0060fe 100644 --- a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -297,9 +292,9 @@ build_info: output: "target/executable/rseqc/rseqc_inner_distance" executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -324,6 +319,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance index eed44f1d..57252795 100755 --- a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance +++ b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance @@ -459,9 +459,9 @@ RUN echo "RSeQC - inner_distance.py: $(inner_distance.py --version | cut -d' ' - LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inner_distance" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_index/.config.vsh.yaml b/target/executable/salmon/salmon_index/.config.vsh.yaml index 74dfef0c..0ab8da57 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -280,9 +275,9 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -307,6 +302,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index 703fc298..40c23bda 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_index" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:28Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/salmon/salmon_quant/.config.vsh.yaml b/target/executable/salmon/salmon_quant/.config.vsh.yaml index 2dd1e4b5..f159c373 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Common input options" arguments: @@ -1176,9 +1171,9 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1203,6 +1198,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 54e0d25e..0f85614c 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -452,9 +452,9 @@ RUN salmon index -v 2>&1 | sed 's/salmon \([0-9.]*\)/salmon: \1/' > /var/softwar LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component salmon salmon_quant" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_collate/.config.vsh.yaml b/target/executable/samtools/samtools_collate/.config.vsh.yaml index 94cdfacf..f63ad491 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -267,9 +262,9 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -294,6 +289,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index 70e763b0..4e36f51a 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_collate" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_faidx/.config.vsh.yaml b/target/executable/samtools/samtools_faidx/.config.vsh.yaml index f55a757e..cd7c6009 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -246,9 +241,9 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -273,6 +268,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index bcb0f510..705ac09d 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_faidx" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fasta/.config.vsh.yaml b/target/executable/samtools/samtools_fasta/.config.vsh.yaml index 48e891bc..33d6f177 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -436,9 +431,9 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -463,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index a46aa64b..8959f231 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fasta" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_fastq/.config.vsh.yaml b/target/executable/samtools/samtools_fastq/.config.vsh.yaml index 63a87ff0..14152ebc 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -436,9 +431,9 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -463,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index 5a18870b..bbd18ae9 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_fastq" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml index 85618e2f..1ae6239e 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -176,9 +171,9 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -203,6 +198,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index fb6fa080..0df4c7e6 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_flagstat" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml index 3914597a..230ea1ce 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -186,9 +181,9 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -213,6 +208,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 08a66f5d..8fff1f0f 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_idxstats" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_index/.config.vsh.yaml b/target/executable/samtools/samtools_index/.config.vsh.yaml index 2fab811b..b8470981 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -192,9 +187,9 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -219,6 +214,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index 0784bfff..c7e21193 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_index" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_sort/.config.vsh.yaml b/target/executable/samtools/samtools_sort/.config.vsh.yaml index 17899dcc..45c07847 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -335,9 +330,9 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -362,6 +357,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index a1c8f526..d702cc24 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_sort" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_stats/.config.vsh.yaml b/target/executable/samtools/samtools_stats/.config.vsh.yaml index b5160d4c..76d327f2 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -404,9 +399,9 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -431,6 +426,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index cddfee64..05ddca45 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_stats" -LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:22Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/samtools/samtools_view/.config.vsh.yaml b/target/executable/samtools/samtools_view/.config.vsh.yaml index 64827b3e..8d57189c 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -668,9 +663,9 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -695,6 +690,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 28915615..f0c2dfed 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -453,9 +453,9 @@ sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component samtools samtools_view" -LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:23Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml index 5e5d9c71..b2edd6df 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -176,9 +176,9 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -203,6 +203,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index 7a67bc63..6ecb7fbc 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -450,9 +450,9 @@ FROM quay.io/biocontainers/seqtk:1.4--he4a0461_2 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_sample" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml index fc03bafa..668b5a6f 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -199,9 +195,9 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -226,6 +222,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index fbe55296..30e66d0a 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -452,9 +452,9 @@ RUN echo $(echo $(seqtk 2>&1) | sed -n 's/.*\(Version: [^ ]*\).*/\1/p') > /var/s LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component seqtk seqtk_subseq" -LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:25Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sgdemux/.config.vsh.yaml b/target/executable/sgdemux/.config.vsh.yaml index 5b09c2fc..35ec7529 100644 --- a/target/executable/sgdemux/.config.vsh.yaml +++ b/target/executable/sgdemux/.config.vsh.yaml @@ -432,9 +432,9 @@ build_info: output: "target/executable/sgdemux" executable: "target/executable/sgdemux/sgdemux" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -459,6 +459,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/sgdemux/sgdemux b/target/executable/sgdemux/sgdemux index 0823f7b6..7ea019dc 100755 --- a/target/executable/sgdemux/sgdemux +++ b/target/executable/sgdemux/sgdemux @@ -457,9 +457,9 @@ echo "sgdemux: $(sgdemux --version | cut -d' ' -f2)" > /var/software_versions.tx LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component sgdemux" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:21Z" LABEL org.opencontainers.image.source="https://github.com/Singular-Genomics/singular-demux" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml index 27cb65c2..50bc2814 100644 --- a/target/executable/snpeff/.config.vsh.yaml +++ b/target/executable/snpeff/.config.vsh.yaml @@ -631,9 +631,9 @@ build_info: output: "target/executable/snpeff" executable: "target/executable/snpeff/snpeff" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -658,6 +658,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff index 4cc1c666..6aa4774d 100755 --- a/target/executable/snpeff/snpeff +++ b/target/executable/snpeff/snpeff @@ -450,9 +450,9 @@ version_trimmed=$(echo "$version" | awk '{print $1, $2}') && \ echo "$version_trimmed" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component snpeff" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:26Z" LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 32d64133..ec7a9226 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -597,9 +597,9 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -624,6 +624,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index f8b86f76..983ba61a 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN echo SortMeRNA: `sortmerna --version | sed -n 's/.*version \([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'` LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2025-05-06T20:11:32Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:19Z" LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_align_reads/.config.vsh.yaml b/target/executable/star/star_align_reads/.config.vsh.yaml index e1ab6ddf..746f0458 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2666,9 +2666,9 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -2693,6 +2693,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index cf3b62c7..d2803a3a 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -475,9 +475,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component star star_align_reads" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/star/star_genome_generate/.config.vsh.yaml b/target/executable/star/star_genome_generate/.config.vsh.yaml index 21fd7c73..c4cbcc8b 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Input" arguments: @@ -336,9 +331,9 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -363,6 +358,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index fbc647eb..2e821c02 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -467,9 +467,9 @@ RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:24Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index ae72d59d..7bb1d314 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Input" arguments: @@ -773,9 +768,9 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -800,6 +795,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 02d07d7c..b6e17dcf 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -452,9 +452,9 @@ RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\ LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa" LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2025-05-06T20:11:42Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:20Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml index 2601be91..a06bb8b0 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -614,9 +609,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -641,6 +636,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup index 1f6d4947..9c2afbaa 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -452,9 +452,9 @@ RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.authors="Emma Rousseau" LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_dedup" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml index 8fc320f3..d9d284ce 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -437,9 +437,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -464,6 +464,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract index 7474be22..829d1f25 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_extract" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index af9ea8e3..2f5c01c9 100644 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -259,9 +259,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_prepareforrsem" executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -286,6 +286,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem index 98bd1e9d..c71488d1 100755 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem @@ -448,9 +448,9 @@ ENTRYPOINT [] RUN umi_tools -v | sed 's/ version//g' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component umi_tools umi_tools_prepareforrsem" -LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z" +LABEL org.opencontainers.image.created="2025-06-16T10:11:29Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60" +LABEL org.opencontainers.image.revision="ad89f437262d32b7cf7afcdfc31b363fc698e8ca" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml index 0bb87193..1785ace1 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -238,9 +233,9 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -265,6 +260,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 8ecc1aec..93d11726 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3322,9 +3314,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3340,6 +3332,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json index 29e2237c..3ad82f07 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json @@ -1,171 +1,102 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_bed2gff", -"description": "The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "bed": { - "type": - "string", - "description": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted", - "help_text": "Type: `file`, required, example: `input.bed`. Input bed file that will be converted." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "source": { - "type": - "string", - "description": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file", - "help_text": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]\n" - - } - - - , - "primary_tag": { - "type": - "string", - "description": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file", - "help_text": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n" - - } - - - , - "inflate_off": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag)", - "help_text": "Type: `boolean_true`, default: `false`. By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag). The type of subfeature created is based on the inflate_type parameter. If you do not want this inflating behaviour you can deactivate it by using the --inflate_off option.\n" - , - "default":false - } - - - , - "inflate_type": { - "type": - "string", - "description": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon]", - "help_text": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. add verbosity", - "help_text": "Type: `boolean_true`, default: `false`. add verbosity" - , - "default":false - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_bed2gff", + "description": "The script takes a bed file as input, and will translate it in gff format. The BED format is described here The script converts 0-based, half-open [start-1, end) bed file to 1-based, closed [start, end] General Feature Format v3 (GFF3).\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "bed": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input bed file that will be converted.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.bed\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GFF file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "source": { + "type": "string", + "description": "The source informs about the tool used to produce the data and is stored in 2nd field of a gff file", + "help_text": "Type: `string`, multiple: `False`, example: `\"Stringtie\"`. " + }, + "primary_tag": { + "type": "string", + "description": "The primary_tag corresponds to the data type and is stored in 3rd field of a gff file", + "help_text": "Type: `string`, multiple: `False`, example: `\"gene\"`. " + }, + "inflate_off": { + "type": "boolean", + "description": "By default we inflate the block fields (blockCount, blockSizes, blockStarts) to create subfeatures of the main feature (primary_tag)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "inflate_type": { + "type": "string", + "description": "Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. " + }, + "verbose": { + "type": "boolean", + "description": "add verbosity", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "config": { + "type": "string", + "format": "path", + "description": "Input agat config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index 1b937b3b..3f918a0c 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -228,9 +223,9 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -255,6 +250,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index 2cda9c89..d87b0a7e 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3315,9 +3307,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3333,6 +3325,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json index ee3a7899..de79d374 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json @@ -1,162 +1,101 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_embl2gff", -"description": "The script takes an EMBL file as input, and will translate it in gff format.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "embl": { - "type": - "string", - "description": "Type: `file`, required, example: `input.embl`. Input EMBL file that will be read", - "help_text": "Type: `file`, required, example: `input.embl`. Input EMBL file that will be read." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file", - "help_text": "Type: `file`, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "emblmygff3": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Means that the EMBL flat file comes from the EMBLmyGFF3 software", - "help_text": "Type: `boolean_true`, default: `false`. Means that the EMBL flat file comes from the EMBLmyGFF3 software. This is an EMBL format dedicated for submission and contains particularity to deal with. This parameter is needed to get a proper sequence id in the GFF3 from an embl made with EMBLmyGFF3.\n" - , - "default":false - } - - - , - "primary_tag": { - "type": - "string", - "description": "Type: List of `string`, example: `tag1;tag2`, multiple_sep: `\";\"`. List of \"primary tag\"", - "help_text": "Type: List of `string`, example: `tag1;tag2`, multiple_sep: `\";\"`. List of \"primary tag\". Useful to discard or keep specific features. Multiple tags must be comma-separated.\n" - - } - - - , - "discard": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Means that primary tags provided by the option \"primary_tag\" will be discarded", - "help_text": "Type: `boolean_true`, default: `false`. Means that primary tags provided by the option \"primary_tag\" will be discarded.\n" - , - "default":false - } - - - , - "keep": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Means that only primary tags provided by the option \"primary_tag\" will be kept", - "help_text": "Type: `boolean_true`, default: `false`. Means that only primary tags provided by the option \"primary_tag\" will be kept.\n" - , - "default":false - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_embl2gff", + "description": "The script takes an EMBL file as input, and will translate it in gff format.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "embl": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input EMBL file that will be read.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.embl\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GFF file", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "emblmygff3": { + "type": "boolean", + "description": "Means that the EMBL flat file comes from the EMBLmyGFF3 software", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "primary_tag": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of \"primary tag\"", + "help_text": "Type: `string`, multiple: `True`, example: `[\"tag1\";\"tag2\"]`. " + }, + "discard": { + "type": "boolean", + "description": "Means that primary tags provided by the option \"primary_tag\" will be discarded.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep": { + "type": "boolean", + "description": "Means that only primary tags provided by the option \"primary_tag\" will be kept.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "config": { + "type": "string", + "format": "path", + "description": "Input agat config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml index ddf46509..43c643ff 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -233,9 +228,9 @@ build_info: output: "target/nextflow/agat/agat_convert_genscan2gff" executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -260,6 +255,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf index ff3bde4e..abda9984 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf +++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3317,9 +3309,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_genscan2gff", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3335,6 +3327,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json index 0a075d38..0667e1e3 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json @@ -1,160 +1,96 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_genscan2gff", -"description": "The script takes a GENSCAN file as input, and will translate it in gff\nformat. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\n**Known problem** \n\nYou must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA\nsequences and does not crash/warn if an header is submited along the\nsequence. e.g If you have an header \"\u003eseq\" s-e-q are seen as the 3 first\nnucleotides of the sequence. Then all prediction location are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). \nI don\u0027t know if there is the same problem elsewhere.)\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "genscan": { - "type": - "string", - "description": "Type: `file`, required. Input genscan bed file that will be converted", - "help_text": "Type: `file`, required. Input genscan bed file that will be converted." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "source": { - "type": - "string", - "description": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file", - "help_text": "Type: `string`, example: `Stringtie`. The source informs about the tool used to produce the data and is stored in 2nd field of a gff file. Example: Stringtie, Maker, Augustus, etc. [default: data]\n" - - } - - - , - "primary_tag": { - "type": - "string", - "description": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file", - "help_text": "Type: `string`, example: `gene`. The primary_tag corresponds to the data type and is stored in 3rd field of a gff file. Example: gene, mRNA, CDS, etc. [default: gene]\n" - - } - - - , - "inflate_type": { - "type": - "string", - "description": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon]", - "help_text": "Type: `string`, example: `exon`. Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. add verbosity", - "help_text": "Type: `boolean_true`, default: `false`. add verbosity" - , - "default":false - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_genscan2gff", + "description": "The script takes a GENSCAN file as input, and will translate it in gff\nformat. The GENSCAN format is described [here](http://genome.crg.es/courses/Bioinformatics2003_genefinding/results/genscan.html).\n\n**Known problem** \n\nYou must have submited only DNA sequence, without any header!! Indeed the tool expects only DNA\nsequences and does not crash/warn if an header is submited along the\nsequence. e.g If you have an header \">seq\" s-e-q are seen as the 3 first\nnucleotides of the sequence. Then all prediction location are shifted\naccordingly. (checked only on the [online version](http://argonaute.mit.edu/GENSCAN.html). \nI don't know if there is the same problem elsewhere.)\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "genscan": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input genscan bed file that will be converted.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GFF file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "source": { + "type": "string", + "description": "The source informs about the tool used to produce the data and is stored in 2nd field of a gff file", + "help_text": "Type: `string`, multiple: `False`, example: `\"Stringtie\"`. " + }, + "primary_tag": { + "type": "string", + "description": "The primary_tag corresponds to the data type and is stored in 3rd field of a gff file", + "help_text": "Type: `string`, multiple: `False`, example: `\"gene\"`. " + }, + "inflate_type": { + "type": "string", + "description": "Feature type (3rd column in gff) created when inflate parameter activated [default: exon].\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. " + }, + "verbose": { + "type": "boolean", + "description": "add verbosity", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml index 27e2c41c..9413bc7c 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -189,9 +184,9 @@ build_info: output: "target/nextflow/agat/agat_convert_mfannot2gff" executable: "target/nextflow/agat/agat_convert_mfannot2gff/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -216,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf index a28af900..cf389721 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf +++ b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3277,9 +3269,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_mfannot2gff", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3295,6 +3287,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json index 13338e44..468fe41c 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json @@ -1,119 +1,75 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_mfannot2gff", -"description": "Conversion utility for MFannot \"masterfile\" annotation produced by the\n[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports\nGFF3 format.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "mfannot": { - "type": - "string", - "description": "Type: `file`, required, example: `input.mfannot`. The mfannot input file", - "help_text": "Type: `file`, required, example: `input.mfannot`. The mfannot input file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.gff.gff`, example: `output.gff`. The GFF output file", - "help_text": "Type: `file`, required, default: `$id.$key.gff.gff`, example: `output.gff`. The GFF output file." - , - "default":"$id.$key.gff.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_mfannot2gff", + "description": "Conversion utility for MFannot \"masterfile\" annotation produced by the\n[MFannot pipeline](http://megasun.bch.umontreal.ca/RNAweasel/). Reports\nGFF3 format.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "mfannot": { + "type": "string", + "format": "path", + "exists": true, + "description": "The mfannot input file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.mfannot\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "description": "The GFF output file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.gff.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.gff.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml index 434af4ec..9e61607f 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -231,9 +226,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -258,6 +253,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index faed45b9..03285710 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3298,9 +3290,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3316,6 +3308,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json index 06054e77..5171a2ca 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json @@ -1,131 +1,89 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_sp_gff2gtf", -"description": "The script aims to convert any GTF/GFF file into a proper GTF file. Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the\nversion selected the script will filter out the features that are not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene) will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA) will be converted into transcript feature. Using the\n\"relax\" option you will produce a GTF-like output keeping all original\nfeature types (3rd column). No modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique identifier for the genomic source of\nthe transcript, which is used to group transcripts into genes. The\ntranscript_id is a unique identifier for the predicted transcript, which\nis used to group features into transcripts.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required, example: `input.gff`. Input GFF/GTF file that will be read", - "help_text": "Type: `file`, required, example: `input.gff`. Input GFF/GTF file that will be read" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gtf`, example: `output.gtf`. Output GTF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gtf`, example: `output.gtf`. Output GTF file. If no output file is specified, the output will be written to STDOUT." - , - "default":"$id.$key.output.gtf" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "gtf_version": { - "type": - "string", - "description": "Type: `string`, example: `3`, choices: ``relax`, `1`, `2`, `2.1`, `2.2`, `2.5`, `3``. Version of the GTF output (1,2,2", - "help_text": "Type: `string`, example: `3`, choices: ``relax`, `1`, `2`, `2.1`, `2.2`, `2.5`, `3``. Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority. \n\n * relax: all feature types are accepted. \n * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr. \n * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine. \n * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon. \n * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR. \n * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon. \n * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron. \n", - "enum": ["relax", "1", "2", "2.1", "2.2", "2.5", "3"] - - - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_sp_gff2gtf", + "description": "The script aims to convert any GTF/GFF file into a proper GTF file. Full\ninformation about the format can be found here:\nhttps://agat.readthedocs.io/en/latest/gxf.html You can choose among 7\ndifferent GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the\nversion selected the script will filter out the features that are not\naccepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene\npseudogene) will be converted into gene feature and every level2 feature\n(e.g mRNA ncRNA) will be converted into transcript feature. Using the\n\"relax\" option you will produce a GTF-like output keeping all original\nfeature types (3rd column). No modification will occur e.g. mRNA to\ntranscript.\n\nTo be fully GTF compliant all feature have a gene_id and a transcript_id\nattribute. The gene_id is unique identifier for the genomic source of\nthe transcript, which is used to group transcripts into genes. The\ntranscript_id is a unique identifier for the predicted transcript, which\nis used to group features into transcripts.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input GFF/GTF file that will be read", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GTF file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gtf\"`, direction: `output`, example: `\"output.gtf\"`. ", + "default": "$id.$key.output.gtf" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "gtf_version": { + "type": "string", + "description": "Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax)", + "help_text": "Type: `string`, multiple: `False`, example: `\"3\"`, choices: ``relax`, `1`, `2`, `2.1`, `2.2`, `2.5`, `3``. ", + "enum": [ + "relax", + "1", + "2", + "2.1", + "2.2", + "2.5", + "3" + ] + }, + "config": { + "type": "string", + "format": "path", + "description": "Input agat config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml index 366a91cd..df0d87eb 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -191,9 +186,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -218,6 +213,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index d8508be9..3309e59f 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3276,9 +3268,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3294,6 +3286,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json index 09998dc3..946f112c 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json @@ -1,119 +1,75 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_sp_gff2tsv", -"description": "The script aims to convert gtf/gff file into tabulated file. Attribute\u0027s\ntags from the 9th column become column titles.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file", - "help_text": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF file. If no output file is specified, the output will be written to STDOUT." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file. By default AGAT takes as input\nagat_config.yaml file from the working directory if any,\notherwise it takes the orignal agat_config.yaml shipped with\nAGAT. To get the agat_config.yaml locally type: \"agat config\n--expose\". The --config option gives you the possibility to use\nyour own AGAT config file (located elsewhere or named\ndifferently). \n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_sp_gff2tsv", + "description": "The script aims to convert gtf/gff file into tabulated file. Attribute's\ntags from the 9th column become column titles.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input GTF/GFF file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GFF file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "String - Input agat config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml index 16d5b883..b5801ab0 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -198,9 +193,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -225,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index a15f6e21..1d1c7357 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3276,9 +3268,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3294,6 +3286,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json index 117ad690..89ce423f 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json @@ -1,119 +1,75 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_convert_sp_gxf2gxf", -"description": "This script fixes and/or standardizes any GTF/GFF file into full sorted\nGTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs, adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes with several parents are duplicated\nwith uniq ID), add missing features when possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described), fix feature locations\n(e.g. check exon is embedded in the parent features mRNA, gene), etc...\n\nAll AGAT\u0027s scripts with the _sp_ prefix use the AGAT parser, before to\nperform any supplementary task. So, it is not necessary to run this\nscript prior the use of any other _sp_ script.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gxf": { - "type": - "string", - "description": "Type: `file`, required, example: `input.gff`. String - Input GTF/GFF file", - "help_text": "Type: `file`, required, example: `input.gff`. String - Input GTF/GFF file. Compressed file with .gz extension is accepted.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. String - Output GFF file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. String - Output GFF file. If no output file is specified, the output will be written to STDOUT.\n" - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: \"agat config --expose\". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_convert_sp_gxf2gxf", + "description": "This script fixes and/or standardizes any GTF/GFF file into full sorted\nGTF/GFF file. It AGAT parser removes duplicate features, fixes\nduplicated IDs, adds missing ID and/or Parent attributes, deflates\nfactorized attributes (attributes with several parents are duplicated\nwith uniq ID), add missing features when possible (e.g. add exon if only\nCDS described, add UTR if CDS and exon described), fix feature locations\n(e.g. check exon is embedded in the parent features mRNA, gene), etc...\n\nAll AGAT's scripts with the _sp_ prefix use the AGAT parser, before to\nperform any supplementary task. So, it is not necessary to run this\nscript prior the use of any other _sp_ script.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gxf": { + "type": "string", + "format": "path", + "exists": true, + "description": "String - Input GTF/GFF file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "String - Output GFF file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "String - Input agat config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml index d730339f..cebe543e 100644 --- a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -189,9 +184,9 @@ build_info: output: "target/nextflow/agat/agat_sp_add_introns" executable: "target/nextflow/agat/agat_sp_add_introns/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -216,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_add_introns/main.nf b/target/nextflow/agat/agat_sp_add_introns/main.nf index eb28d5cd..7315ebfc 100644 --- a/target/nextflow/agat/agat_sp_add_introns/main.nf +++ b/target/nextflow/agat/agat_sp_add_introns/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3279,9 +3271,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_add_introns", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3297,6 +3289,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json b/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json index ef12e523..91439cb8 100644 --- a/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json @@ -1,119 +1,75 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_sp_add_introns", -"description": "Add intronic elements to a gtf/gff file without intron features.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file", - "help_text": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF3 file", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output GFF3 file." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option \ngives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_sp_add_introns", + "description": "Add intronic elements to a gtf/gff file without intron features.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input GTF/GFF file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output GFF3 file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml index c1f34fc5..4f9e0cbb 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -239,9 +234,9 @@ build_info: output: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list" executable: "target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -266,6 +261,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf index aa58b712..b069b72b 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3326,9 +3318,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_filter_feature_from_kill_list", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3344,6 +3336,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json index 035d050c..40173a45 100644 --- a/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_filter_feature_from_kill_list/nextflow_schema.json @@ -1,160 +1,101 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_sp_filter_feature_from_kill_list", -"description": "Remove features based on a kill list. The default behaviour is to look at the features\u0027s ID. \nIf the feature has an ID (case insensitive) listed among the kill list it will be removed.\nRemoving a level1 or level2 feature will automatically remove all linked subfeatures, and \nremoving all children of a feature will automatically remove this feature too.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required. Input GFF3 file that will be read", - "help_text": "Type: `file`, required. Input GFF3 file that will be read." - - } - - - , - "kill_list": { - "type": - "string", - "description": "Type: `file`, required, example: `kill_list.txt`. Text file containing the kill list", - "help_text": "Type: `file`, required, example: `kill_list.txt`. Text file containing the kill list. One value per line." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Path to the output GFF file that contains filtered features", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Path to the output GFF file that contains filtered features. \n" - , - "default":"$id.$key.output" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "type": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Primary tag option, case insensitive, list", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Primary tag option, case insensitive, list. Allow to specify the feature types that \nwill be handled. \n\nYou can specify a specific feature by giving its primary tag name (column 3) as: \n\n * cds\n * Gene\n * mRNA\n \nYou can specify directly all the feature of a particular\nlevel: \n\n * level2=mRNA,ncRNA,tRNA,etc \n * level3=CDS,exon,UTR,etc. \n\nBy default all features are taken into account. Fill the option with the value \"all\" will \nhave the same behaviour.\n" - - } - - - , - "attribute": { - "type": - "string", - "description": "Type: `string`, example: `ID`. Attribute tag to specify the attribute to analyse", - "help_text": "Type: `string`, example: `ID`. Attribute tag to specify the attribute to analyse. Case sensitive. Default: ID\n" - - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT.\nThe `--config` option gives you the possibility to use your own AGAT config file (located \nelsewhere or named differently).\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Verbose option for debugging purpose", - "help_text": "Type: `boolean_true`, default: `false`. Verbose option for debugging purpose." - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_sp_filter_feature_from_kill_list", + "description": "Remove features based on a kill list. The default behaviour is to look at the features's ID. \nIf the feature has an ID (case insensitive) listed among the kill list it will be removed.\nRemoving a level1 or level2 feature will automatically remove all linked subfeatures, and \nremoving all children of a feature will automatically remove this feature too.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input GFF3 file that will be read.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "kill_list": { + "type": "string", + "format": "path", + "exists": true, + "description": "Text file containing the kill list", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"kill_list.txt\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Path to the output GFF file that contains filtered features", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Primary tag option, case insensitive, list", + "help_text": "Type: `string`, multiple: `True`. " + }, + "attribute": { + "type": "string", + "description": "Attribute tag to specify the attribute to analyse", + "help_text": "Type: `string`, multiple: `False`, example: `\"ID\"`. " + }, + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + }, + "verbose": { + "type": "boolean", + "description": "Verbose option for debugging purpose.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml index bb9cc2ba..7606cbc9 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -187,9 +182,9 @@ build_info: output: "target/nextflow/agat/agat_sp_merge_annotations" executable: "target/nextflow/agat/agat_sp_merge_annotations/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -214,6 +209,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_merge_annotations/main.nf b/target/nextflow/agat/agat_sp_merge_annotations/main.nf index 78cb7245..f12a59e9 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/main.nf +++ b/target/nextflow/agat/agat_sp_merge_annotations/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3276,9 +3268,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_merge_annotations", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3294,6 +3286,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json b/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json index 3e405d46..10715a0c 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json @@ -1,119 +1,78 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_sp_merge_annotations", -"description": "Merge different gff annotation files into one. It uses the AGAT parser that takes care of\nduplicated names and fixes other oddities met in those files.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: List of `file`, required, example: `input1.gff;input2.gff`, multiple_sep: `\";\"`. Input GTF/GFF file(s)", - "help_text": "Type: List of `file`, required, example: `input1.gff;input2.gff`, multiple_sep: `\";\"`. Input GTF/GFF file(s).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output gff3 file where the gene incriminated will be writen", - "help_text": "Type: `file`, required, default: `$id.$key.output.gff`, example: `output.gff`. Output gff3 file where the gene incriminated will be writen." - , - "default":"$id.$key.output.gff" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. \nThe `--config` option gives you the possibility to use your own AGAT config file (located\nelsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_sp_merge_annotations", + "description": "Merge different gff annotation files into one. It uses the AGAT parser that takes care of\nduplicated names and fixes other oddities met in those files.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Input GTF/GFF file(s).\n", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input1.gff;input2.gff\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output gff3 file where the gene incriminated will be writen.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.output.gff" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml index bcaa1d50..96a88983 100644 --- a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -234,9 +229,9 @@ build_info: output: "target/nextflow/agat/agat_sp_statistics" executable: "target/nextflow/agat/agat_sp_statistics/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -261,6 +256,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sp_statistics/main.nf b/target/nextflow/agat/agat_sp_statistics/main.nf index af1cf12c..bcfd8011 100644 --- a/target/nextflow/agat/agat_sp_statistics/main.nf +++ b/target/nextflow/agat/agat_sp_statistics/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3326,9 +3318,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_statistics", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3344,6 +3336,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json b/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json index 286849d7..108e8143 100644 --- a/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json @@ -1,160 +1,97 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_sp_statistics", -"description": "The script provides exhaustive statistics of a gft/gff file. \n\nIf you have isoforms in your file, even if correct, some values calculated\nmight sounds incoherent: e.g. total length mRNA can be superior than the\ngenome size. Because all isoforms length is added... It is why by\ndefault we always compute the statistics twice when there are isoforms,\nonce with the isoforms, once without (In that case we keep the longest\nisoform per locus).\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file", - "help_text": "Type: `file`, required, example: `input.gff`. Input GTF/GFF file." - - } - - - , - "gs_fasta": { - "type": - "string", - "description": "Type: `file`, example: `genome.fasta`. Genome size directly from a fasta file to compute more statistics", - "help_text": "Type: `file`, example: `genome.fasta`. Genome size directly from a fasta file to compute more statistics.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. The file where the results will be written", - "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. The file where the results will be written.\n" - , - "default":"$id.$key.output.txt" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "plot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When this option is used, an histogram of distribution of the features will be printed in pdf files", - "help_text": "Type: `boolean_true`, default: `false`. When this option is used, an histogram of distribution of the features will be printed in pdf files.\n" - , - "default":false - } - - - , - "gs_size": { - "type": - "integer", - "description": "Type: `integer`, example: `1000000`. Genome size in nucleotides to compute more statistics", - "help_text": "Type: `integer`, example: `1000000`. Genome size in nucleotides to compute more statistics.\n" - - } - - - , - "verbose": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Verbose option", - "help_text": "Type: `integer`, example: `1`. Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing verbosity.\n" - - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config`\noption gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_sp_statistics", + "description": "The script provides exhaustive statistics of a gft/gff file. \n\nIf you have isoforms in your file, even if correct, some values calculated\nmight sounds incoherent: e.g. total length mRNA can be superior than the\ngenome size. Because all isoforms length is added... It is why by\ndefault we always compute the statistics twice when there are isoforms,\nonce with the isoforms, once without (In that case we keep the longest\nisoform per locus).\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input GTF/GFF file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.gff\"`. " + }, + "gs_fasta": { + "type": "string", + "format": "path", + "description": "Genome size directly from a fasta file to compute more statistics.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The file where the results will be written.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ", + "default": "$id.$key.output.txt" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "plot": { + "type": "boolean", + "description": "When this option is used, an histogram of distribution of the features will be printed in pdf files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gs_size": { + "type": "integer", + "description": "Genome size in nucleotides to compute more statistics.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. " + }, + "verbose": { + "type": "integer", + "description": "Verbose option", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml index af02f112..d80851c4 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "leila@data-intuitive.com" github: "Leila011" linkedin: "leilapaquay" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Software Developer" argument_groups: - name: "Inputs" arguments: @@ -230,9 +225,9 @@ build_info: output: "target/nextflow/agat/agat_sq_stat_basic" executable: "target/nextflow/agat/agat_sq_stat_basic/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -257,6 +252,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/agat/agat_sq_stat_basic/main.nf b/target/nextflow/agat/agat_sq_stat_basic/main.nf index 63060d41..b2ac31af 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/main.nf +++ b/target/nextflow/agat/agat_sq_stat_basic/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "leila@data-intuitive.com", "github" : "Leila011", "linkedin" : "leilapaquay" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Software Developer" - } - ] + } } } ], @@ -3312,9 +3304,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sq_stat_basic", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3330,6 +3322,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json b/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json index 90bd4e80..37c5773e 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json +++ b/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json @@ -1,150 +1,95 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "agat_sq_stat_basic", -"description": "The script aims to provide basic statistics of a gtf/gff file.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "gff": { - "type": - "string", - "description": "Type: List of `file`, required, example: `input.gff`, multiple_sep: `\";\"`. Input GTF/GFF file", - "help_text": "Type: List of `file`, required, example: `input.gff`, multiple_sep: `\";\"`. Input GTF/GFF file.\n" - - } - - - , - "genome_size": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type", - "help_text": "Type: `integer`, example: `10000`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide an INTEGER. Or you can also pass a fasta file using the argument --genome_size_fasta. If both are provided, only the value of --genome_size will be considered.\n" - - } - - - , - "genome_size_fasta": { - "type": - "string", - "description": "Type: `file`, example: `genome.fasta`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type", - "help_text": "Type: `file`, example: `genome.fasta`. That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type. You can provide the genome in fasta format. Or you can also pass the size directly as an integer using the argument --genome_size. If you provide the fasta, the genome size will be calculated on the fly. If both are provided, only the value of --genome_size will be considered.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. Output file", - "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `output.txt`. Output file. The result is in tabulate format.\n" - , - "default":"$id.$key.output.txt" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "inflate": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Inflate the statistics taking into account feature with\nmulti-parents", - "help_text": "Type: `boolean_true`, default: `false`. Inflate the statistics taking into account feature with\nmulti-parents. Indeed to avoid redundant information, some gff\nfactorize identical features. e.g: one exon used in two\ndifferent isoform will be defined only once, and will have\nmultiple parent. By default the script count such feature only\nonce. Using the inflate option allows to count the feature and\nits size as many time there are parents.\n" - , - "default":false - } - - - , - "config": { - "type": - "string", - "description": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file", - "help_text": "Type: `file`, example: `custom_agat_config.yaml`. AGAT config file. By default AGAT takes the original agat_config.yaml shipped with AGAT. The `--config` option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "agat_sq_stat_basic", + "description": "The script aims to provide basic statistics of a gtf/gff file.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "gff": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Input GTF/GFF file.\n", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input.gff\"]`. " + }, + "genome_size": { + "type": "integer", + "description": "That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "genome_size_fasta": { + "type": "string", + "format": "path", + "description": "That input is designed to know the genome size in order to calculate the percentage of the genome represented by each kind of feature type", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ", + "default": "$id.$key.output.txt" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "inflate": { + "type": "boolean", + "description": "Inflate the statistics taking into account feature with\nmulti-parents", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "config": { + "type": "string", + "format": "path", + "description": "AGAT config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_agat_config.yaml\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 75eae161..27ca0f22 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -709,9 +709,9 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -736,6 +736,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index 0b119e73..a9aedd14 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3822,9 +3822,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3840,6 +3840,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/arriba/nextflow_schema.json b/target/nextflow/arriba/nextflow_schema.json index 5dc1e112..190a60dc 100644 --- a/target/nextflow/arriba/nextflow_schema.json +++ b/target/nextflow/arriba/nextflow_schema.json @@ -1,465 +1,273 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "arriba", -"description": "Detect gene fusions from RNA-Seq data", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "bam": { - "type": - "string", - "description": "Type: `file`, required, example: `Aligned.out.bam`. File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned", - "help_text": "Type: `file`, required, example: `Aligned.out.bam`. File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned.out.sam). Arriba extracts candidate reads from this file.\n" - - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`, required, example: `assembly.fa`. FastA file with genome sequence (assembly)", - "help_text": "Type: `file`, required, example: `assembly.fa`. FastA file with genome sequence (assembly). The file may be gzip-compressed. An \nindex with the file extension .fai must exist only if CRAM files are processed.\n" - - } - - - , - "gene_annotation": { - "type": - "string", - "description": "Type: `file`, required, example: `annotation.gtf`. GTF file with gene annotation", - "help_text": "Type: `file`, required, example: `annotation.gtf`. GTF file with gene annotation. The file may be gzip-compressed.\n" - - } - - - , - "known_fusions": { - "type": - "string", - "description": "Type: `file`, example: `known_fusions.tsv`. File containing known/recurrent fusions", - "help_text": "Type: `file`, example: `known_fusions.tsv`. File containing known/recurrent fusions. Some cancer entities are often \ncharacterized by fusions between the same pair of genes. In order to boost \nsensitivity, a list of known fusions can be supplied using this parameter. The list \nmust contain two columns with the names of the fused genes, separated by tabs.\n" - - } - - - , - "blacklist": { - "type": - "string", - "description": "Type: `file`, example: `blacklist.tsv`. File containing blacklisted events (recurrent artifacts and transcripts \nobserved in healthy tissue)", - "help_text": "Type: `file`, example: `blacklist.tsv`. File containing blacklisted events (recurrent artifacts and transcripts \nobserved in healthy tissue).\n" - - } - - - , - "structural_variants": { - "type": - "string", - "description": "Type: `file`, example: `structural_variants_from_WGS.tsv`. Tab-separated file with coordinates of structural variants found using \nwhole-genome sequencing data", - "help_text": "Type: `file`, example: `structural_variants_from_WGS.tsv`. Tab-separated file with coordinates of structural variants found using \nwhole-genome sequencing data. These coordinates serve to increase sensitivity \ntowards weakly expressed fusions and to eliminate fusions with low evidence. \n" - - } - - - , - "tags": { - "type": - "string", - "description": "Type: `file`, example: `tags.tsv`. Tab-separated file containing fusions to annotate with tags in the \u0027tags\u0027 column", - "help_text": "Type: `file`, example: `tags.tsv`. Tab-separated file containing fusions to annotate with tags in the \u0027tags\u0027 column. \nThe first two columns specify the genes; the third column specifies the tag. The \nfile may be gzip-compressed. \n" - - } - - - , - "protein_domains": { - "type": - "string", - "description": "Type: `file`, example: `protein_domains.gff3`. File in GFF3 format containing coordinates of the protein domains of genes", - "help_text": "Type: `file`, example: `protein_domains.gff3`. File in GFF3 format containing coordinates of the protein domains of genes. The\nprotein domains retained in a fusion are listed in the column\n\u0027retained_protein_domains\u0027. The file may be gzip-compressed.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "fusions": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.fusions.tsv`, example: `fusions.tsv`. Output file with fusions that have passed all filters", - "help_text": "Type: `file`, required, default: `$id.$key.fusions.tsv`, example: `fusions.tsv`. Output file with fusions that have passed all filters.\n" - , - "default":"$id.$key.fusions.tsv" - } - - - , - "fusions_discarded": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fusions_discarded.tsv`, example: `fusions.discarded.tsv`. Output file with fusions that were discarded due to filtering", - "help_text": "Type: `file`, default: `$id.$key.fusions_discarded.tsv`, example: `fusions.discarded.tsv`. Output file with fusions that were discarded due to filtering. \n" - , - "default":"$id.$key.fusions_discarded.tsv" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "max_genomic_breakpoint_distance": { - "type": - "string", - "description": "Type: `long`. When a file with genomic breakpoints obtained via \nwhole-genome sequencing is supplied via the --structural_variants\nparameter, this parameter determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic breakpoint to consider it as a \nrelated event", - "help_text": "Type: `long`. When a file with genomic breakpoints obtained via \nwhole-genome sequencing is supplied via the --structural_variants\nparameter, this parameter determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic breakpoint to consider it as a \nrelated event. For events inside genes, the \ndistance is added to the end of the gene; for \nintergenic events, the distance threshold is \napplied as is. Default: 100000.\n" - - } - - - , - "strandedness": { - "type": - "string", - "description": "Type: `string`, choices: ``auto`, `yes`, `no`, `reverse``. Whether a strand-specific protocol was used for library preparation, \nand if so, the type of strandedness (auto/yes/no/reverse)", - "help_text": "Type: `string`, choices: ``auto`, `yes`, `no`, `reverse``. Whether a strand-specific protocol was used for library preparation, \nand if so, the type of strandedness (auto/yes/no/reverse). When \nunstranded data is processed, the strand can sometimes be inferred from \nsplice-patterns. But in unclear situations, stranded data helps \nresolve ambiguities. Default: auto\n", - "enum": ["auto", "yes", "no", "reverse"] - - - } - - - , - "interesting_contigs": { - "type": - "string", - "description": "Type: List of `string`, example: `1;2;AC_*;NC_*`, multiple_sep: `\";\"`. List of interesting contigs", - "help_text": "Type: List of `string`, example: `1;2;AC_*;NC_*`, multiple_sep: `\";\"`. List of interesting contigs. Fusions between genes \non other contigs are ignored. Contigs can be specified with or without the \nprefix \"chr\". Asterisks (*) are treated as wild-cards. \nDefault: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*\n" - - } - - - , - "viral_contigs": { - "type": - "string", - "description": "Type: List of `string`, example: `AC_*;NC_*`, multiple_sep: `\";\"`. List of viral contigs", - "help_text": "Type: List of `string`, example: `AC_*;NC_*`, multiple_sep: `\";\"`. List of viral contigs. Asterisks (*) are treated as \nwild-cards.\nDefault: AC_* NC_*\n" - - } - - - , - "disable_filters": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`, choices: ``homologs`, `low_entropy`, `isoforms`, `top_expressed_viral_contigs`, `viral_contigs`, `uninteresting_contigs`, `non_coding_neighbors`, `mismatches`, `duplicates`, `no_genomic_support`, `genomic_support`, `intronic`, `end_to_end`, `relative_support`, `low_coverage_viral_contigs`, `merge_adjacent`, `mismappers`, `multimappers`, `same_gene`, `long_gap`, `internal_tandem_duplication`, `small_insert_size`, `read_through`, `inconsistently_clipped`, `intragenic_exonic`, `marginal_read_through`, `spliced`, `hairpin`, `blacklist`, `min_support`, `select_best`, `in_vitro`, `short_anchor`, `known_fusions`, `no_coverage`, `homopolymer`, `many_spliced``. List of filters to disable", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`, choices: ``homologs`, `low_entropy`, `isoforms`, `top_expressed_viral_contigs`, `viral_contigs`, `uninteresting_contigs`, `non_coding_neighbors`, `mismatches`, `duplicates`, `no_genomic_support`, `genomic_support`, `intronic`, `end_to_end`, `relative_support`, `low_coverage_viral_contigs`, `merge_adjacent`, `mismappers`, `multimappers`, `same_gene`, `long_gap`, `internal_tandem_duplication`, `small_insert_size`, `read_through`, `inconsistently_clipped`, `intragenic_exonic`, `marginal_read_through`, `spliced`, `hairpin`, `blacklist`, `min_support`, `select_best`, `in_vitro`, `short_anchor`, `known_fusions`, `no_coverage`, `homopolymer`, `many_spliced``. List of filters to disable. By default all filters are \nenabled. \n" - - } - - - , - "max_e_value": { - "type": - "number", - "description": "Type: `double`. Arriba estimates the number of fusions with a given number of supporting \nreads which one would expect to see by random chance", - "help_text": "Type: `double`. Arriba estimates the number of fusions with a given number of supporting \nreads which one would expect to see by random chance. If the expected number \nof fusions (e-value) is higher than this threshold, the fusion is \ndiscarded by the \u0027relative_support\u0027 filter. Note: Increasing this \nthreshold can dramatically increase the number of false positives and may \nincrease the runtime of resource-intensive steps. Fractional values are \npossible. Default: 0.300000 \n" - - } - - - , - "min_supporting_reads": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. The \u0027min_support\u0027 filter discards all fusions with fewer than \nthis many supporting reads (split reads and discordant mates \ncombined)", - "help_text": "Type: `integer`, example: `2`. The \u0027min_support\u0027 filter discards all fusions with fewer than \nthis many supporting reads (split reads and discordant mates \ncombined). Default: 2 \n" - - } - - - , - "max_mismappers": { - "type": - "number", - "description": "Type: `double`, example: `0.8`. When more than this fraction of supporting reads turns out to be \nmismappers, the \u0027mismappers\u0027 filter discards the fusion", - "help_text": "Type: `double`, example: `0.8`. When more than this fraction of supporting reads turns out to be \nmismappers, the \u0027mismappers\u0027 filter discards the fusion. Default: \n0.800000\n" - - } - - - , - "max_homolog_identity": { - "type": - "number", - "description": "Type: `double`, example: `0.3`. Genes with more than the given fraction of sequence identity are \nconsidered homologs and removed by the \u0027homologs\u0027 filter", - "help_text": "Type: `double`, example: `0.3`. Genes with more than the given fraction of sequence identity are \nconsidered homologs and removed by the \u0027homologs\u0027 filter. \nDefault: 0.300000 \n" - - } - - - , - "homopolymer_length": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. The \u0027homopolymer\u0027 filter removes breakpoints adjacent to \nhomopolymers of the given length or more", - "help_text": "Type: `integer`, example: `6`. The \u0027homopolymer\u0027 filter removes breakpoints adjacent to \nhomopolymers of the given length or more. Default: 6\n" - - } - - - , - "read_through_distance": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. The \u0027read_through\u0027 filter removes read-through fusions \nwhere the breakpoints are less than the given distance away \nfrom each other", - "help_text": "Type: `integer`, example: `10000`. The \u0027read_through\u0027 filter removes read-through fusions \nwhere the breakpoints are less than the given distance away \nfrom each other. Default: 10000 \n" - - } - - - , - "min_anchor_length": { - "type": - "integer", - "description": "Type: `integer`, example: `23`. Alignment artifacts are often characterized by split reads coming \nfrom only one gene and no discordant mates", - "help_text": "Type: `integer`, example: `23`. Alignment artifacts are often characterized by split reads coming \nfrom only one gene and no discordant mates. Moreover, the split \nreads only align to a short stretch in one of the genes. The \n\u0027short_anchor\u0027 filter removes these fusions. This parameter sets \nthe threshold in bp for what the filter considers short. Default: 23 \n" - - } - - - , - "many_spliced_events": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. The \u0027many_spliced\u0027 filter recovers fusions between genes that \nhave at least this many spliced breakpoints", - "help_text": "Type: `integer`, example: `4`. The \u0027many_spliced\u0027 filter recovers fusions between genes that \nhave at least this many spliced breakpoints. Default: 4\n" - - } - - - , - "max_kmer_content": { - "type": - "number", - "description": "Type: `double`, example: `0.6`. The \u0027low_entropy\u0027 filter removes reads with repetitive 3-mers", - "help_text": "Type: `double`, example: `0.6`. The \u0027low_entropy\u0027 filter removes reads with repetitive 3-mers. If \nthe 3-mers make up more than the given fraction of the sequence, then \nthe read is discarded. Default: 0.600000 \n" - - } - - - , - "max_mismatch_pvalue": { - "type": - "number", - "description": "Type: `double`, example: `0.05`. The \u0027mismatches\u0027 filter uses a binomial model to calculate a \np-value for observing a given number of mismatches in a read", - "help_text": "Type: `double`, example: `0.05`. The \u0027mismatches\u0027 filter uses a binomial model to calculate a \np-value for observing a given number of mismatches in a read. If \nthe number of mismatches is too high, the read is discarded. \nDefault: 0.010000 \n" - - } - - - , - "fragment_length": { - "type": - "integer", - "description": "Type: `integer`, example: `200`. When paired-end data is given, the fragment length is estimated \nautomatically and this parameter has no effect", - "help_text": "Type: `integer`, example: `200`. When paired-end data is given, the fragment length is estimated \nautomatically and this parameter has no effect. But when single-end \ndata is given, the mean fragment length should be specified to \neffectively filter fusions that arise from hairpin structures. \nDefault: 200 \n" - - } - - - , - "max_reads": { - "type": - "integer", - "description": "Type: `integer`, example: `300`. Subsample fusions with more than the given number of supporting reads", - "help_text": "Type: `integer`, example: `300`. Subsample fusions with more than the given number of supporting reads. This \nimproves performance without compromising sensitivity, as long as the \nthreshold is high. Counting of supporting reads beyond the threshold is \ninaccurate, obviously. Default: 300 \n" - - } - - - , - "quantile": { - "type": - "number", - "description": "Type: `double`, example: `0.998`. Highly expressed genes are prone to produce artifacts during library \npreparation", - "help_text": "Type: `double`, example: `0.998`. Highly expressed genes are prone to produce artifacts during library \npreparation. Genes with an expression above the given quantile are eligible \nfor filtering by the \u0027in_vitro\u0027 filter. Default: 0.998000\n" - - } - - - , - "exonic_fraction": { - "type": - "number", - "description": "Type: `double`, example: `0.33`. The breakpoints of false-positive predictions of intragenic events \nare often both in exons", - "help_text": "Type: `double`, example: `0.33`. The breakpoints of false-positive predictions of intragenic events \nare often both in exons. True predictions are more likely to have at \nleast one breakpoint in an intron, because introns are larger. If the \nfraction of exonic sequence between two breakpoints is smaller than \nthe given fraction, the \u0027intragenic_exonic\u0027 filter discards the \nevent. Default: 0.330000 \n" - - } - - - , - "top_n": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. Only report viral integration sites of the top N most highly expressed viral \ncontigs", - "help_text": "Type: `integer`, example: `5`. Only report viral integration sites of the top N most highly expressed viral \ncontigs. Default: 5\n" - - } - - - , - "covered_fraction": { - "type": - "number", - "description": "Type: `double`, example: `0.05`. Ignore virally associated events if the virus is not fully \nexpressed, i", - "help_text": "Type: `double`, example: `0.05`. Ignore virally associated events if the virus is not fully \nexpressed, i.e., less than the given fraction of the viral contig is \ntranscribed. Default: 0.050000 \n" - - } - - - , - "max_itd_length": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. Maximum length of internal tandem duplications", - "help_text": "Type: `integer`, example: `100`. Maximum length of internal tandem duplications. Note: Increasing \nthis value beyond the default can impair performance and lead to many \nfalse positives. Default: 100 \n" - - } - - - , - "min_itd_allele_fraction": { - "type": - "number", - "description": "Type: `double`, example: `0.07`. Required fraction of supporting reads to report an internal \ntandem duplication", - "help_text": "Type: `double`, example: `0.07`. Required fraction of supporting reads to report an internal \ntandem duplication. Default: 0.070000 \n" - - } - - - , - "min_itd_supporting_reads": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. Required absolute number of supporting reads to report an \ninternal tandem duplication", - "help_text": "Type: `integer`, example: `10`. Required absolute number of supporting reads to report an \ninternal tandem duplication. Default: 10 \n" - - } - - - , - "skip_duplicate_marking": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a \npreceding program using the BAM_FDUP flag", - "help_text": "Type: `boolean_true`, default: `false`. Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a \npreceding program using the BAM_FDUP flag. This makes sense when unique molecular \nidentifiers (UMI) are used.\n" - , - "default":false - } - - - , - "extra_information": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. To reduce the runtime and file size, by default, the columns \u0027fusion_transcript\u0027, \n\u0027peptide_sequence\u0027, and \u0027read_identifiers\u0027 are left empty in the file containing \ndiscarded fusion candidates (see parameter -O)", - "help_text": "Type: `boolean_true`, default: `false`. To reduce the runtime and file size, by default, the columns \u0027fusion_transcript\u0027, \n\u0027peptide_sequence\u0027, and \u0027read_identifiers\u0027 are left empty in the file containing \ndiscarded fusion candidates (see parameter -O). When this flag is set, this extra \ninformation is reported in the discarded fusions file.\n" - , - "default":false - } - - - , - "fill_gaps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If assembly of the fusion transcript sequence from the supporting reads is incomplete \n(denoted as \u0027", - "help_text": "Type: `boolean_true`, default: `false`. If assembly of the fusion transcript sequence from the supporting reads is incomplete \n(denoted as \u0027...\u0027), fill the gaps using the assembly sequence wherever possible. \n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "arriba", + "description": "Detect gene fusions from RNA-Seq data", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "bam": { + "type": "string", + "format": "path", + "exists": true, + "description": "File in SAM/BAM/CRAM format with main alignments as generated by STAR\n(Aligned.out.sam)", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"Aligned.out.bam\"`. " + }, + "genome": { + "type": "string", + "format": "path", + "exists": true, + "description": "FastA file with genome sequence (assembly)", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"assembly.fa\"`. " + }, + "gene_annotation": { + "type": "string", + "format": "path", + "exists": true, + "description": "GTF file with gene annotation", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"annotation.gtf\"`. " + }, + "known_fusions": { + "type": "string", + "format": "path", + "description": "File containing known/recurrent fusions", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"known_fusions.tsv\"`. " + }, + "blacklist": { + "type": "string", + "format": "path", + "description": "File containing blacklisted events (recurrent artifacts and transcripts \nobserved in healthy tissue).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"blacklist.tsv\"`. " + }, + "structural_variants": { + "type": "string", + "format": "path", + "description": "Tab-separated file with coordinates of structural variants found using \nwhole-genome sequencing data", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"structural_variants_from_WGS.tsv\"`. " + }, + "tags": { + "type": "string", + "format": "path", + "description": "Tab-separated file containing fusions to annotate with tags in the 'tags' column", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"tags.tsv\"`. " + }, + "protein_domains": { + "type": "string", + "format": "path", + "description": "File in GFF3 format containing coordinates of the protein domains of genes", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"protein_domains.gff3\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "fusions": { + "type": "string", + "format": "path", + "description": "Output file with fusions that have passed all filters.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.fusions.tsv\"`, direction: `output`, example: `\"fusions.tsv\"`. ", + "default": "$id.$key.fusions.tsv" + }, + "fusions_discarded": { + "type": "string", + "format": "path", + "description": "Output file with fusions that were discarded due to filtering", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fusions_discarded.tsv\"`, direction: `output`, example: `\"fusions.discarded.tsv\"`. ", + "default": "$id.$key.fusions_discarded.tsv" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "max_genomic_breakpoint_distance": { + "type": "string", + "description": "When a file with genomic breakpoints obtained via \nwhole-genome sequencing is supplied via the --structural_variants\nparameter, this parameter determines how far a \ngenomic breakpoint may be away from a \ntranscriptomic breakpoint to consider it as a \nrelated event", + "help_text": "Type: `long`, multiple: `False`. " + }, + "strandedness": { + "type": "string", + "description": "Whether a strand-specific protocol was used for library preparation, \nand if so, the type of strandedness (auto/yes/no/reverse)", + "help_text": "Type: `string`, multiple: `False`, choices: ``auto`, `yes`, `no`, `reverse``. ", + "enum": [ + "auto", + "yes", + "no", + "reverse" + ] + }, + "interesting_contigs": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of interesting contigs", + "help_text": "Type: `string`, multiple: `True`, example: `[\"1\";\"2\";\"AC_*\";\"NC_*\"]`. " + }, + "viral_contigs": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of viral contigs", + "help_text": "Type: `string`, multiple: `True`, example: `[\"AC_*\";\"NC_*\"]`. " + }, + "disable_filters": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of filters to disable", + "help_text": "Type: `string`, multiple: `True`, choices: ``homologs`, `low_entropy`, `isoforms`, `top_expressed_viral_contigs`, `viral_contigs`, `uninteresting_contigs`, `non_coding_neighbors`, `mismatches`, `duplicates`, `no_genomic_support`, `genomic_support`, `intronic`, `end_to_end`, `relative_support`, `low_coverage_viral_contigs`, `merge_adjacent`, `mismappers`, `multimappers`, `same_gene`, `long_gap`, `internal_tandem_duplication`, `small_insert_size`, `read_through`, `inconsistently_clipped`, `intragenic_exonic`, `marginal_read_through`, `spliced`, `hairpin`, `blacklist`, `min_support`, `select_best`, `in_vitro`, `short_anchor`, `known_fusions`, `no_coverage`, `homopolymer`, `many_spliced``. " + }, + "max_e_value": { + "type": "number", + "description": "Arriba estimates the number of fusions with a given number of supporting \nreads which one would expect to see by random chance", + "help_text": "Type: `double`, multiple: `False`. " + }, + "min_supporting_reads": { + "type": "integer", + "description": "The 'min_support' filter discards all fusions with fewer than \nthis many supporting reads (split reads and discordant mates \ncombined)", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "max_mismappers": { + "type": "number", + "description": "When more than this fraction of supporting reads turns out to be \nmismappers, the 'mismappers' filter discards the fusion", + "help_text": "Type: `double`, multiple: `False`, example: `0.8`. " + }, + "max_homolog_identity": { + "type": "number", + "description": "Genes with more than the given fraction of sequence identity are \nconsidered homologs and removed by the 'homologs' filter", + "help_text": "Type: `double`, multiple: `False`, example: `0.3`. " + }, + "homopolymer_length": { + "type": "integer", + "description": "The 'homopolymer' filter removes breakpoints adjacent to \nhomopolymers of the given length or more", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "read_through_distance": { + "type": "integer", + "description": "The 'read_through' filter removes read-through fusions \nwhere the breakpoints are less than the given distance away \nfrom each other", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "min_anchor_length": { + "type": "integer", + "description": "Alignment artifacts are often characterized by split reads coming \nfrom only one gene and no discordant mates", + "help_text": "Type: `integer`, multiple: `False`, example: `23`. " + }, + "many_spliced_events": { + "type": "integer", + "description": "The 'many_spliced' filter recovers fusions between genes that \nhave at least this many spliced breakpoints", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "max_kmer_content": { + "type": "number", + "description": "The 'low_entropy' filter removes reads with repetitive 3-mers", + "help_text": "Type: `double`, multiple: `False`, example: `0.6`. " + }, + "max_mismatch_pvalue": { + "type": "number", + "description": "The 'mismatches' filter uses a binomial model to calculate a \np-value for observing a given number of mismatches in a read", + "help_text": "Type: `double`, multiple: `False`, example: `0.05`. " + }, + "fragment_length": { + "type": "integer", + "description": "When paired-end data is given, the fragment length is estimated \nautomatically and this parameter has no effect", + "help_text": "Type: `integer`, multiple: `False`, example: `200`. " + }, + "max_reads": { + "type": "integer", + "description": "Subsample fusions with more than the given number of supporting reads", + "help_text": "Type: `integer`, multiple: `False`, example: `300`. " + }, + "quantile": { + "type": "number", + "description": "Highly expressed genes are prone to produce artifacts during library \npreparation", + "help_text": "Type: `double`, multiple: `False`, example: `0.998`. " + }, + "exonic_fraction": { + "type": "number", + "description": "The breakpoints of false-positive predictions of intragenic events \nare often both in exons", + "help_text": "Type: `double`, multiple: `False`, example: `0.33`. " + }, + "top_n": { + "type": "integer", + "description": "Only report viral integration sites of the top N most highly expressed viral \ncontigs", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "covered_fraction": { + "type": "number", + "description": "Ignore virally associated events if the virus is not fully \nexpressed, i.e., less than the given fraction of the viral contig is \ntranscribed", + "help_text": "Type: `double`, multiple: `False`, example: `0.05`. " + }, + "max_itd_length": { + "type": "integer", + "description": "Maximum length of internal tandem duplications", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "min_itd_allele_fraction": { + "type": "number", + "description": "Required fraction of supporting reads to report an internal \ntandem duplication", + "help_text": "Type: `double`, multiple: `False`, example: `0.07`. " + }, + "min_itd_supporting_reads": { + "type": "integer", + "description": "Required absolute number of supporting reads to report an \ninternal tandem duplication", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "skip_duplicate_marking": { + "type": "boolean", + "description": "Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a \npreceding program using the BAM_FDUP flag", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "extra_information": { + "type": "boolean", + "description": "To reduce the runtime and file size, by default, the columns 'fusion_transcript', \n'peptide_sequence', and 'read_identifiers' are left empty in the file containing \ndiscarded fusion candidates (see parameter -O)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fill_gaps": { + "type": "boolean", + "description": "If assembly of the fusion transcript sequence from the supporting reads is incomplete \n(denoted as '...'), fill the gaps using the assembly sequence wherever possible", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bases2fastq/.config.vsh.yaml b/target/nextflow/bases2fastq/.config.vsh.yaml index dda9da8d..ecd98894 100644 --- a/target/nextflow/bases2fastq/.config.vsh.yaml +++ b/target/nextflow/bases2fastq/.config.vsh.yaml @@ -397,9 +397,9 @@ build_info: output: "target/nextflow/bases2fastq" executable: "target/nextflow/bases2fastq/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -424,6 +424,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bases2fastq/main.nf b/target/nextflow/bases2fastq/main.nf index 5a88d2fa..b7fa81a8 100644 --- a/target/nextflow/bases2fastq/main.nf +++ b/target/nextflow/bases2fastq/main.nf @@ -3514,9 +3514,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bases2fastq", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3532,6 +3532,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bases2fastq/nextflow_schema.json b/target/nextflow/bases2fastq/nextflow_schema.json index d59d797b..1b614462 100644 --- a/target/nextflow/bases2fastq/nextflow_schema.json +++ b/target/nextflow/bases2fastq/nextflow_schema.json @@ -1,394 +1,232 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bases2fastq", -"description": "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.\n", -"type": "object", -"definitions": { - - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "chemistry_version": { - "type": - "string", - "description": "Type: `string`. Run parameters override, chemistry version", - "help_text": "Type: `string`. Run parameters override, chemistry version." - - } - - - , - "demux_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate demux files and indexing stats without generating FASTQ\n", - "help_text": "Type: `boolean_true`, default: `false`. Generate demux files and indexing stats without generating FASTQ\n" - , - "default":false - } - - - , - "detect_adapters": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Detect adapters sequences, overriding any sequences present in run manifest", - "help_text": "Type: `boolean_true`, default: `false`. Detect adapters sequences, overriding any sequences present in run manifest.\n" - , - "default":false - } - - - , - "error_on_missing": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Terminate execution for a missing file (by default, missing files are\nskipped and execution continues)", - "help_text": "Type: `boolean_true`, default: `false`. Terminate execution for a missing file (by default, missing files are\nskipped and execution continues). Also set by --strict.\n" - , - "default":false - } - - - , - "exclude_tile": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Regex matching tile names to exclude", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Regex matching tile names to exclude. This flag can be specified multiple times. (e.g. L1.*C0[23]S.)\n" - - } - - - , - "filter_mask": { - "type": - "string", - "description": "Type: `string`. Run parameters override, custom pass filter mask", - "help_text": "Type: `string`. Run parameters override, custom pass filter mask.\n" - - } - - - , - "flowcell_id": { - "type": - "string", - "description": "Type: `string`. Run parameters override, flowcell ID", - "help_text": "Type: `string`. Run parameters override, flowcell ID.\n" - - } - - - , - "force_index_orientation": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not attempt to find orientation for I1/I2 reads (reverse complement)", - "help_text": "Type: `boolean_true`, default: `false`. Do not attempt to find orientation for I1/I2 reads (reverse complement).\nUse orientation given in run manifest.\n" - , - "default":false - } - - - , - "group_fastq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Group all FASTQ/stats/metrics for a project are in the project folder", - "help_text": "Type: `boolean_true`, default: `false`. Group all FASTQ/stats/metrics for a project are in the project folder.\n" - , - "default":false - } - - - , - "i1_cycles": { - "type": - "integer", - "description": "Type: `integer`. Run parameters override, I1 cycles", - "help_text": "Type: `integer`. Run parameters override, I1 cycles.\n" - - } - - - , - "i2_cycles": { - "type": - "integer", - "description": "Type: `integer`. Run parameters override, I2 cycles\n", - "help_text": "Type: `integer`. Run parameters override, I2 cycles\n" - - } - - - , - "include_tile": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Regex matching tile names to include", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Regex matching tile names to include. This flag\ncan be specified multiple times. (e.g. L1.*C0[23]S.)\n" - - } - - - , - "kit_configuration": { - "type": - "string", - "description": "Type: `string`. Run parameters override, kit configuration", - "help_text": "Type: `string`. Run parameters override, kit configuration.\n" - - } - - - , - "legacy_fastq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Legacy naming for FASTQ files (e", - "help_text": "Type: `boolean_true`, default: `false`. Legacy naming for FASTQ files (e.g. SampleName_S1_L001_R1_001.fastq.gz)\n" - , - "default":false - } - - - , - "log_level": { - "type": - "string", - "description": "Type: `string`, example: `INFO`, choices: ``DEBUG`, `INFO`, `WARNING`, `ERROR``. Severity level for logging", - "help_text": "Type: `string`, example: `INFO`, choices: ``DEBUG`, `INFO`, `WARNING`, `ERROR``. Severity level for logging.\n", - "enum": ["DEBUG", "INFO", "WARNING", "ERROR"] - - - } - - - , - "no_error_on_invalid": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip invalid files and continue execution", - "help_text": "Type: `boolean_true`, default: `false`. Skip invalid files and continue execution. Overridden by --strict options\n" - , - "default":false - } - - - , - "no_projects": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable project directories\n", - "help_text": "Type: `boolean_true`, default: `false`. Disable project directories\n" - , - "default":false - } - - - , - "num_unassigned": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. Max Number of unassigned sequences to report", - "help_text": "Type: `integer`, example: `30`. Max Number of unassigned sequences to report.\n" - - } - - - , - "preparation_workflow": { - "type": - "string", - "description": "Type: `string`. Run parameters override, preparation workflow", - "help_text": "Type: `string`. Run parameters override, preparation workflow. \n" - - } - - - , - "qc_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Quickly generate run stats for single tile without generating FASTQ", - "help_text": "Type: `boolean_true`, default: `false`. Quickly generate run stats for single tile without generating FASTQ.\nUse --include_tile/--exclude_tile to define custom tile set.\n" - , - "default":false - } - - - , - "r1_cycles": { - "type": - "integer", - "description": "Type: `integer`. Run parameters override, R1 cycles", - "help_text": "Type: `integer`. Run parameters override, R1 cycles.\n" - - } - - - , - "r2_cycles": { - "type": - "integer", - "description": "Type: `integer`. Run parameters override, R2 cycles", - "help_text": "Type: `integer`. Run parameters override, R2 cycles.\n" - - } - - - , - "split_lanes": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Split FASTQ files by lane", - "help_text": "Type: `boolean_true`, default: `false`. Split FASTQ files by lane.\n" - , - "default":false - } - - - , - "strict": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In strict mode any invalid or missing input file will terminate execution \n(overrides no_error_on_invalid and sets --error_on_missing)\n", - "help_text": "Type: `boolean_true`, default: `false`. In strict mode any invalid or missing input file will terminate execution \n(overrides no_error_on_invalid and sets --error_on_missing)\n" - , - "default":false - } - - -} -}, - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "analysis_directory": { - "type": - "string", - "description": "Type: `file`, required, example: `input`. Location of analysis directory", - "help_text": "Type: `file`, required, example: `input`. Location of analysis directory" - - } - - - , - "run_manifest": { - "type": - "string", - "description": "Type: `file`. Location of run manifest to use instead of default RunManifest", - "help_text": "Type: `file`. Location of run manifest to use instead of default RunManifest.csv found in analysis directory" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_directory": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Location to save output fastqs", - "help_text": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Location to save output fastqs" - , - "default":"$id.$key.output_directory" - } - - - , - "report": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.report`. Output location for the HTML report", - "help_text": "Type: `file`, default: `$id.$key.report`. Output location for the HTML report" - , - "default":"$id.$key.report" - } - - - , - "logs": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Directory containing log files", - "help_text": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Directory containing log files" - , - "default":"$id.$key.logs" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bases2fastq", + "description": "Bases2Fastq demultiplexes sequencing data generated by Element Biosciences instruments and converts base calls into FASTQ files.\n", + "type": "object", + "$defs": { + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "chemistry_version": { + "type": "string", + "description": "Run parameters override, chemistry version.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "demux_only": { + "type": "boolean", + "description": "Generate demux files and indexing stats without generating FASTQ\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "detect_adapters": { + "type": "boolean", + "description": "Detect adapters sequences, overriding any sequences present in run manifest.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "error_on_missing": { + "type": "boolean", + "description": "Terminate execution for a missing file (by default, missing files are\nskipped and execution continues)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "exclude_tile": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Regex matching tile names to exclude", + "help_text": "Type: `string`, multiple: `True`. " + }, + "filter_mask": { + "type": "string", + "description": "Run parameters override, custom pass filter mask.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "flowcell_id": { + "type": "string", + "description": "Run parameters override, flowcell ID.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "force_index_orientation": { + "type": "boolean", + "description": "Do not attempt to find orientation for I1/I2 reads (reverse complement).\nUse orientation given in run manifest.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "group_fastq": { + "type": "boolean", + "description": "Group all FASTQ/stats/metrics for a project are in the project folder.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "i1_cycles": { + "type": "integer", + "description": "Run parameters override, I1 cycles.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "i2_cycles": { + "type": "integer", + "description": "Run parameters override, I2 cycles\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "include_tile": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Regex matching tile names to include", + "help_text": "Type: `string`, multiple: `True`. " + }, + "kit_configuration": { + "type": "string", + "description": "Run parameters override, kit configuration.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "legacy_fastq": { + "type": "boolean", + "description": "Legacy naming for FASTQ files (e.g", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "log_level": { + "type": "string", + "description": "Severity level for logging.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"INFO\"`, choices: ``DEBUG`, `INFO`, `WARNING`, `ERROR``. ", + "enum": [ + "DEBUG", + "INFO", + "WARNING", + "ERROR" + ] + }, + "no_error_on_invalid": { + "type": "boolean", + "description": "Skip invalid files and continue execution", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_projects": { + "type": "boolean", + "description": "Disable project directories\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_unassigned": { + "type": "integer", + "description": "Max Number of unassigned sequences to report.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `30`. " + }, + "preparation_workflow": { + "type": "string", + "description": "Run parameters override, preparation workflow", + "help_text": "Type: `string`, multiple: `False`. " + }, + "qc_only": { + "type": "boolean", + "description": "Quickly generate run stats for single tile without generating FASTQ.\nUse --include_tile/--exclude_tile to define custom tile set.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "r1_cycles": { + "type": "integer", + "description": "Run parameters override, R1 cycles.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "r2_cycles": { + "type": "integer", + "description": "Run parameters override, R2 cycles.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "split_lanes": { + "type": "boolean", + "description": "Split FASTQ files by lane.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "strict": { + "type": "boolean", + "description": "In strict mode any invalid or missing input file will terminate execution \n(overrides no_error_on_invalid and sets --error_on_missing)\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/input" + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "analysis_directory": { + "type": "string", + "format": "path", + "exists": true, + "description": "Location of analysis directory", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input\"`. " + }, + "run_manifest": { + "type": "string", + "format": "path", + "description": "Location of run manifest to use instead of default RunManifest.csv found in analysis directory", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output_directory": { + "type": "string", + "format": "path", + "description": "Location to save output fastqs", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_directory\"`, direction: `output`, example: `\"fastq_dir\"`. ", + "default": "$id.$key.output_directory" + }, + "report": { + "type": "string", + "format": "path", + "description": "Output location for the HTML report", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.report\"`, direction: `output`. ", + "default": "$id.$key.report" + }, + "logs": { + "type": "string", + "format": "path", + "description": "Directory containing log files", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.logs\"`, direction: `output`, example: `\"logs_dir\"`. ", + "default": "$id.$key.logs" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml index 9786818b..11d3cc72 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -371,9 +371,9 @@ build_info: output: "target/nextflow/bbmap/bbmap_bbsplit" executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -398,6 +398,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf index b00fe978..f6329438 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf @@ -3450,9 +3450,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bbmap/bbmap_bbsplit", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3468,6 +3468,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json index 7b8b1edd..2e45479c 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json +++ b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json @@ -1,321 +1,203 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bbmap_bbsplit", -"description": "Split sequencing reads by mapping them to multiple references simultaneously.", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "id": { - "type": - "string", - "description": "Type: `string`. Sample ID", - "help_text": "Type: `string`. Sample ID" - - } - - - , - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?", - "help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?" - , - "default":false - } - - - , - "input": { - "type": - "string", - "description": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"", - "help_text": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"." - - } - - - , - "ref": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\"", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\". The primary reference should be specified first." - - } - - - , - "only_build_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If set, only builds the index", - "help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed." - , - "default":false - } - - - , - "build": { - "type": - "string", - "description": "Type: `file`. Index to be used for mapping", - "help_text": "Type: `file`. Index to be used for mapping. \n" - - } - - - , - "qin": { - "type": - "string", - "description": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset", - "help_text": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if\nnot specified.\n" - - } - - - , - "interleaved": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping", - "help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n" - , - "default":false - } - - - , - "maxindel": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this", - "help_text": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this. Lower is faster. Set to \u003e=100k for RNA-seq.\n" - - } - - - , - "minratio": { - "type": - "number", - "description": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site", - "help_text": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site. Higher is faster.\n" - - } - - - , - "minhits": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites", - "help_text": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites. Higher is faster.\n" - - } - - - , - "ambiguous": { - "type": - "string", - "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations)", - "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).\n * best Use the first best site (Default)\n * toss Consider unmapped\n * random Select one top-scoring site randomly\n * all Retain all top-scoring sites. Does not work yet with SAM output\n", - "enum": ["best", "toss", "random", "all"] - - - } - - - , - "ambiguous2": { - "type": - "string", - "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references", - "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references.\nNormal \u0027ambiguous=\u0027 controls behavior on all ambiguous reads;\nAmbiguous2 excludes reads that map ambiguously within a single reference.\n * best Use the first best site (Default)\n * toss Consider unmapped\n * all Write a copy to the output for each reference to which it maps\n * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps\n", - "enum": ["best", "toss", "all", "split"] - - - } - - - , - "qtrim": { - "type": - "string", - "description": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping", - "help_text": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping. Options are \u0027l\u0027 (left), \u0027r\u0027 (right), and \u0027lr\u0027 (both).\n", - "enum": ["l", "r", "lr"] - - - } - - - , - "untrim": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping", - "help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings." - , - "default":false - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index", - "help_text": "Type: `file`, default: `$id.$key.index`, example: `BBSplit_index`. Location to write the index.\n" - , - "default":"$id.$key.index" - } - - - , - "fastq_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1", - "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n" - , - "default":"$id.$key.fastq_1.fastq" - } - - - , - "fastq_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2", - "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n" - , - "default":"$id.$key.fastq_2.fastq" - } - - - , - "sam2bam": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file", - "help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n" - , - "default":"$id.$key.sam2bam.sh" - } - - - , - "scafstats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file", - "help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n" - , - "default":"$id.$key.scafstats.txt" - } - - - , - "refstats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file", - "help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n" - , - "default":"$id.$key.refstats.txt" - } - - - , - "nzo": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage", - "help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage." - , - "default":false - } - - - , - "bbmap_args": { - "type": - "string", - "description": "Type: `string`. Additional arguments from BBMap to pass to BBSplit", - "help_text": "Type: `string`. Additional arguments from BBMap to pass to BBSplit.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bbmap_bbsplit", + "description": "Split sequencing reads by mapping them to multiple references simultaneously.", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "id": { + "type": "string", + "description": "Sample ID", + "help_text": "Type: `string`, multiple: `False`. " + }, + "paired": { + "type": "boolean", + "description": "Paired fastq files or not?", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fastq files, either one or two (paired), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads.fastq\"]`. " + }, + "ref": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Reference FASTA files, separated by \";\"", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "only_build_index": { + "type": "boolean", + "description": "If set, only builds the index", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "build": { + "type": "string", + "format": "path", + "description": "Index to be used for mapping", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "qin": { + "type": "string", + "description": "Set to 33 or 64 to specify input quality value ASCII offset", + "help_text": "Type: `string`, multiple: `False`. " + }, + "interleaved": { + "type": "boolean", + "description": "True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "maxindel": { + "type": "integer", + "description": "Don't look for indels longer than this", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "minratio": { + "type": "number", + "description": "Fraction of max alignment score required to keep a site", + "help_text": "Type: `double`, multiple: `False`, example: `0.56`. " + }, + "minhits": { + "type": "integer", + "description": "Minimum number of seed hits required for candidate sites", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "ambiguous": { + "type": "string", + "description": "Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).\n * best Use the first best site (Default)\n * toss Consider unmapped\n * random Select one top-scoring site randomly\n * all Retain all top-scoring sites", + "help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `random`, `all``. ", + "enum": [ + "best", + "toss", + "random", + "all" + ] + }, + "ambiguous2": { + "type": "string", + "description": "Set behavior only for reads that map ambiguously to multiple different references.\nNormal 'ambiguous=' controls behavior on all ambiguous reads;\nAmbiguous2 excludes reads that map ambiguously within a single reference.\n * best Use the first best site (Default)\n * toss Consider unmapped\n * all Write a copy to the output for each reference to which it maps\n * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `all`, `split``. ", + "enum": [ + "best", + "toss", + "all", + "split" + ] + }, + "qtrim": { + "type": "string", + "description": "Quality-trim ends to Q5 before mapping", + "help_text": "Type: `string`, multiple: `False`, choices: ``l`, `r`, `lr``. ", + "enum": [ + "l", + "r", + "lr" + ] + }, + "untrim": { + "type": "boolean", + "description": "Undo trimming after mapping", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "string", + "format": "path", + "description": "Location to write the index.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.index\"`, direction: `output`, example: `\"BBSplit_index\"`. ", + "default": "$id.$key.index" + }, + "fastq_1": { + "type": "string", + "format": "path", + "description": "Output file for read 1.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_1.fastq\"`, direction: `output`, example: `\"read_out1.fastq\"`. ", + "default": "$id.$key.fastq_1.fastq" + }, + "fastq_2": { + "type": "string", + "format": "path", + "description": "Output file for read 2.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_2.fastq\"`, direction: `output`, example: `\"read_out2.fastq\"`. ", + "default": "$id.$key.fastq_2.fastq" + }, + "sam2bam": { + "type": "string", + "format": "path", + "description": "Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sam2bam.sh\"`, direction: `output`, example: `\"script.sh\"`. ", + "default": "$id.$key.sam2bam.sh" + }, + "scafstats": { + "type": "string", + "format": "path", + "description": "Write statistics on how many reads mapped to which scaffold to this file.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.scafstats.txt\"`, direction: `output`, example: `\"scaffold_stats.txt\"`. ", + "default": "$id.$key.scafstats.txt" + }, + "refstats": { + "type": "string", + "format": "path", + "description": "Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.refstats.txt\"`, direction: `output`, example: `\"reference_stats.txt\"`. ", + "default": "$id.$key.refstats.txt" + }, + "nzo": { + "type": "boolean", + "description": "Only print lines with nonzero coverage.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bbmap_args": { + "type": "string", + "description": "Additional arguments from BBMap to pass to BBSplit.\n", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml index 40b5a726..19859785 100644 --- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -472,9 +468,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_annotate" executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -499,6 +495,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf index ac68f5e8..7471dd8c 100644 --- a/target/nextflow/bcftools/bcftools_annotate/main.nf +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -3047,14 +3047,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3565,9 +3558,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_annotate", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3583,6 +3576,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json index c2a06bda..f40d2bcc 100644 --- a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json @@ -1,369 +1,230 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcftools_annotate", -"description": "Add or remove annotations from a VCF/BCF file.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file", - "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output annotated file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output annotated file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\nFor more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n", - "properties": { - - - "annotations": { - "type": - "string", - "description": "Type: `file`. VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ", - "help_text": "Type: `file`. VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ . \n" - - } - - - , - "columns": { - "type": - "string", - "description": "Type: `string`. List of columns in the annotation file, e", - "help_text": "Type: `string`. List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. \nSee man page for details.\n" - - } - - - , - "columns_file": { - "type": - "string", - "description": "Type: `file`. Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE]", - "help_text": "Type: `file`. Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].\n" - - } - - - , - "exclude": { - "type": - "string", - "description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Exclude sites for which the expression is true", - "help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" - - } - - - , - "force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. continue even when parsing errors, such as undefined tags, are encountered", - "help_text": "Type: `boolean_true`, default: `false`. continue even when parsing errors, such as undefined tags, are encountered. \nNote this can be an unsafe operation and can result in corrupted BCF files. \nIf this option is used, make sure to sanity check the result thoroughly.\n" - , - "default":false - } - - - , - "header_line": { - "type": - "string", - "description": "Type: `string`. Header line which should be appended to the VCF header, can be given multiple times", - "help_text": "Type: `string`. Header line which should be appended to the VCF header, can be given multiple times.\n" - - } - - - , - "header_lines": { - "type": - "string", - "description": "Type: `file`. File with header lines to append to the VCF header", - "help_text": "Type: `file`. File with header lines to append to the VCF header.\nFor example:\n ##INFO=\u003cID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header line\"\u003e\n ##INFO=\u003cID=STRING_TAG,Number=1,Type=String,Description=\"Yet another header line\"\u003e\n" - - } - - - , - "set_id": { - "type": - "string", - "description": "Type: `string`. Set ID column using a `bcftools query`-like expression, see man page for details", - "help_text": "Type: `string`. Set ID column using a `bcftools query`-like expression, see man page for details.\n" - - } - - - , - "include": { - "type": - "string", - "description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true", - "help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" - - } - - - , - "keep_sites": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Leave --include/--exclude sites unchanged instead of discarding them", - "help_text": "Type: `boolean_true`, default: `false`. Leave --include/--exclude sites unchanged instead of discarding them.\n" - , - "default":false - } - - - , - "merge_logic": { - "type": - "string", - "description": "Type: `string`. When multiple regions overlap a single record, this option defines how to treat multiple annotation values", - "help_text": "Type: `string`. When multiple regions overlap a single record, this option defines how to treat multiple annotation values.\nSee man page for more details.\n" - - } - - - , - "mark_sites": { - "type": - "string", - "description": "Type: `string`. Annotate sites which are present (\"+\") or absent (\"-\") in the -a file with a new INFO/TAG flag", - "help_text": "Type: `string`. Annotate sites which are present (\"+\") or absent (\"-\") in the -a file with a new INFO/TAG flag.\n" - - } - - - , - "min_overlap": { - "type": - "string", - "description": "Type: `string`. Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)", - "help_text": "Type: `string`. Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.\n" - - } - - - , - "no_version": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the output VCF header", - "help_text": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the output VCF header.\n" - , - "default":false - } - - - , - "output_type": { - "type": - "string", - "description": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "help_text": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "enum": ["u", "z", "b", "v"] - - - } - - - , - "pair_logic": { - "type": - "string", - "description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `exact``. Controls how to match records from the annotation file to the target VCF", - "help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `exact``. Controls how to match records from the annotation file to the target VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces the former uninuitive --collapse. \nSee Common Options for more.\n", - "enum": ["snps", "indels", "both", "all", "some", "exact"] - - - } - - - , - "regions": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" - - } - - - , - "regions_file": { - "type": - "string", - "description": "Type: `file`. Restrict to regions listed in a file", - "help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n" - - } - - - , - "regions_overlap": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - - , - "rename_annotations": { - "type": - "string", - "description": "Type: `file`. Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT", - "help_text": "Type: `file`. Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n" - - } - - - , - "rename_chromosomes": { - "type": - "string", - "description": "Type: `file`. Rename chromosomes according to the map in file, with \"old_name new_name\\n\" pairs \nseparated by whitespaces, each on a separate line", - "help_text": "Type: `file`. Rename chromosomes according to the map in file, with \"old_name new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n" - - } - - - , - "samples": { - "type": - "string", - "description": "Type: `string`. Subset of samples to annotate", - "help_text": "Type: `string`. Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" - - } - - - , - "samples_file": { - "type": - "string", - "description": "Type: `file`. Subset of samples to annotate in file format", - "help_text": "Type: `file`. Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n" - - } - - - , - "single_overlaps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use this option to keep memory requirements low with very large annotation files", - "help_text": "Type: `boolean_true`, default: `false`. Use this option to keep memory requirements low with very large annotation files. \nNote, however, that this comes at a cost, only single overlapping intervals are considered in this mode. \nThis was the default mode until the commit af6f0c9 (Feb 24 2019).\n" - , - "default":false - } - - - , - "remove": { - "type": - "string", - "description": "Type: `string`. List of annotations to remove", - "help_text": "Type: `string`. List of annotations to remove. \nUse \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\" (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\".\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcftools_annotate", + "description": "Add or remove annotations from a VCF/BCF file.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Input VCF/BCF file.", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output annotated file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\nFor more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n", + "properties": { + "annotations": { + "type": "string", + "format": "path", + "description": "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "columns": { + "type": "string", + "description": "List of columns in the annotation file, e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "columns_file": { + "type": "string", + "format": "path", + "description": "Read -c columns from FILE, one name per row, with optional --merge_logic TYPE: NAME[ TYPE].\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "exclude": { + "type": "string", + "description": "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL >= 30 && DP >= 10\"`. " + }, + "force": { + "type": "boolean", + "description": "continue even when parsing errors, such as undefined tags, are encountered", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "header_line": { + "type": "string", + "description": "Header line which should be appended to the VCF header, can be given multiple times.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "header_lines": { + "type": "string", + "format": "path", + "description": "File with header lines to append to the VCF header.\nFor example:\n ##INFO=\n ##INFO=\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "set_id": { + "type": "string", + "description": "Set ID column using a `bcftools query`-like expression, see man page for details.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "include": { + "type": "string", + "description": "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL >= 30 && DP >= 10\"`. " + }, + "keep_sites": { + "type": "boolean", + "description": "Leave --include/--exclude sites unchanged instead of discarding them.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "merge_logic": { + "type": "string", + "description": "When multiple regions overlap a single record, this option defines how to treat multiple annotation values.\nSee man page for more details.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "mark_sites": { + "type": "string", + "description": "Annotate sites which are present (\"+\") or absent (\"-\") in the -a file with a new INFO/TAG flag.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "min_overlap": { + "type": "string", + "description": "Minimum overlap required as a fraction of the variant in the annotation -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_version": { + "type": "boolean", + "description": "Do not append version and command line information to the output VCF header.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_type": { + "type": "string", + "description": "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``u`, `z`, `b`, `v``. ", + "enum": [ + "u", + "z", + "b", + "v" + ] + }, + "pair_logic": { + "type": "string", + "description": "Controls how to match records from the annotation file to the target VCF", + "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `some`, `exact``. ", + "enum": [ + "snps", + "indels", + "both", + "all", + "some", + "exact" + ] + }, + "regions": { + "type": "string", + "description": "Restrict to comma-separated list of regions", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "regions_file": { + "type": "string", + "format": "path", + "description": "Restrict to regions listed in a file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "regions_overlap": { + "type": "string", + "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + }, + "rename_annotations": { + "type": "string", + "format": "path", + "description": "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "rename_chromosomes": { + "type": "string", + "format": "path", + "description": "Rename chromosomes according to the map in file, with \"old_name new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "samples": { + "type": "string", + "description": "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "samples_file": { + "type": "string", + "format": "path", + "description": "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "single_overlaps": { + "type": "boolean", + "description": "Use this option to keep memory requirements low with very large annotation files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "remove": { + "type": "string", + "description": "List of annotations to remove", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml index ffee3c83..96d17f4e 100644 --- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -338,9 +334,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_concat" executable: "target/nextflow/bcftools/bcftools_concat/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -365,6 +361,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf index 8ffe8d95..949743a9 100644 --- a/target/nextflow/bcftools/bcftools_concat/main.nf +++ b/target/nextflow/bcftools/bcftools_concat/main.nf @@ -3047,14 +3047,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3437,9 +3430,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_concat", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3455,6 +3448,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json index 5889e67f..db79851f 100644 --- a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json @@ -1,273 +1,178 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcftools_concat", -"description": "Concatenate or combine VCF/BCF files. All source files must have the same sample\ncolumns appearing in the same order. The program can be used, for example, to\nconcatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\nVCF into one. The input files must be sorted by chr and position. The files\nmust be given in the correct order to produce sorted VCF on output unless\nthe -a, --allow-overlaps option is specified. With the --naive option, the files\nare concatenated without being recompressed, which is very fast.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Input VCF/BCF files to concatenate", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Input VCF/BCF files to concatenate." - - } - - - , - "file_list": { - "type": - "string", - "description": "Type: `file`. Read the list of VCF/BCF files from a file, one file name per line", - "help_text": "Type: `file`. Read the list of VCF/BCF files from a file, one file name per line." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output concatenated VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output concatenated VCF/BCF file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "allow_overlaps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. First coordinate of the next file can precede last record of the current file", - "help_text": "Type: `boolean_true`, default: `false`. First coordinate of the next file can precede last record of the current file.\n" - , - "default":false - } - - - , - "compact_PS": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not output PS tag at each site, only at the start of a new phase set block", - "help_text": "Type: `boolean_true`, default: `false`. Do not output PS tag at each site, only at the start of a new phase set block.\n" - , - "default":false - } - - - , - "remove_duplicates": { - "type": - "string", - "description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. Output duplicate records present in multiple files only once: \u003csnps|indels|both|all|exact\u003e", - "help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. Output duplicate records present in multiple files only once: \u003csnps|indels|both|all|exact\u003e.\n \n", - "enum": ["snps", "indels", "both", "all", "exact", "none"] - - - } - - - , - "ligate": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ligate phased VCFs by matching phase at overlapping haplotypes", - "help_text": "Type: `boolean_true`, default: `false`. Ligate phased VCFs by matching phase at overlapping haplotypes." - , - "default":false - } - - - , - "ligate_force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ligate even non-overlapping chunks, keep all sites", - "help_text": "Type: `boolean_true`, default: `false`. Ligate even non-overlapping chunks, keep all sites." - , - "default":false - } - - - , - "ligate_warn": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Drop sites in imperfect overlaps", - "help_text": "Type: `boolean_true`, default: `false`. Drop sites in imperfect overlaps." - , - "default":false - } - - - , - "no_version": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the header", - "help_text": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the header." - , - "default":false - } - - - , - "naive": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Concatenate files without recompression, a header check compatibility is performed", - "help_text": "Type: `boolean_true`, default: `false`. Concatenate files without recompression, a header check compatibility is performed." - , - "default":false - } - - - , - "naive_force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Same as --naive, but header compatibility is not checked", - "help_text": "Type: `boolean_true`, default: `false`. Same as --naive, but header compatibility is not checked. \nDangerous, use with caution.\n" - , - "default":false - } - - - , - "output_type": { - "type": - "string", - "description": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "help_text": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "enum": ["u", "z", "b", "v"] - - - } - - - , - "min_PQ": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. Break phase set if phasing quality is lower than \u003cint\u003e", - "help_text": "Type: `integer`, example: `30`. Break phase set if phasing quality is lower than \u003cint\u003e." - - } - - - , - "regions": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" - - } - - - , - "regions_file": { - "type": - "string", - "description": "Type: `file`. Restrict to regions listed in a file", - "help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n" - - } - - - , - "regions_overlap": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcftools_concat", + "description": "Concatenate or combine VCF/BCF files. All source files must have the same sample\ncolumns appearing in the same order. The program can be used, for example, to\nconcatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\nVCF into one. The input files must be sorted by chr and position. The files\nmust be given in the correct order to produce sorted VCF on output unless\nthe -a, --allow-overlaps option is specified. With the --naive option, the files\nare concatenated without being recompressed, which is very fast.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input VCF/BCF files to concatenate.", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "file_list": { + "type": "string", + "format": "path", + "description": "Read the list of VCF/BCF files from a file, one file name per line.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output concatenated VCF/BCF file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "allow_overlaps": { + "type": "boolean", + "description": "First coordinate of the next file can precede last record of the current file.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "compact_PS": { + "type": "boolean", + "description": "Do not output PS tag at each site, only at the start of a new phase set block.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "remove_duplicates": { + "type": "string", + "description": "Output duplicate records present in multiple files only once: .\n \n", + "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. ", + "enum": [ + "snps", + "indels", + "both", + "all", + "exact", + "none" + ] + }, + "ligate": { + "type": "boolean", + "description": "Ligate phased VCFs by matching phase at overlapping haplotypes.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ligate_force": { + "type": "boolean", + "description": "Ligate even non-overlapping chunks, keep all sites.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ligate_warn": { + "type": "boolean", + "description": "Drop sites in imperfect overlaps.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_version": { + "type": "boolean", + "description": "Do not append version and command line information to the header.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "naive": { + "type": "boolean", + "description": "Concatenate files without recompression, a header check compatibility is performed.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "naive_force": { + "type": "boolean", + "description": "Same as --naive, but header compatibility is not checked", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_type": { + "type": "string", + "description": "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``u`, `z`, `b`, `v``. ", + "enum": [ + "u", + "z", + "b", + "v" + ] + }, + "min_PQ": { + "type": "integer", + "description": "Break phase set if phasing quality is lower than .", + "help_text": "Type: `integer`, multiple: `False`, example: `30`. " + }, + "regions": { + "type": "string", + "description": "Restrict to comma-separated list of regions", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "regions_file": { + "type": "string", + "format": "path", + "description": "Restrict to regions listed in a file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "regions_overlap": { + "type": "string", + "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml index 16290b22..e7f95bac 100644 --- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -419,9 +415,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_norm" executable: "target/nextflow/bcftools/bcftools_norm/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -446,6 +442,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf index fed2346c..1b79671a 100644 --- a/target/nextflow/bcftools/bcftools_norm/main.nf +++ b/target/nextflow/bcftools/bcftools_norm/main.nf @@ -3047,14 +3047,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3530,9 +3523,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_norm", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3548,6 +3541,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json index 7f18c71d..f7bcc49f 100644 --- a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json @@ -1,328 +1,227 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcftools_norm", -"description": "Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; \nrecover multiallelics from multiple rows. \n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input VCF/BCF file", - "help_text": "Type: `file`, required. Input VCF/BCF file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output normalized VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output normalized VCF/BCF file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "atomize": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Decompose complex variants (e", - "help_text": "Type: `boolean_true`, default: `false`. Decompose complex variants (e.g., MNVs become consecutive SNVs).\n" - , - "default":false - } - - - , - "atom_overlaps": { - "type": - "string", - "description": "Type: `string`, choices: ``.`, `*``. Use the star allele (*) for overlapping alleles or set to missing (", - "help_text": "Type: `string`, choices: ``.`, `*``. Use the star allele (*) for overlapping alleles or set to missing (.).\n", - "enum": [".", "*"] - - - } - - - , - "check_ref": { - "type": - "string", - "description": "Type: `string`, choices: ``e`, `w`, `x`, `s``. Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites", - "help_text": "Type: `string`, choices: ``e`, `w`, `x`, `s``. Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n", - "enum": ["e", "w", "x", "s"] - - - } - - - , - "remove_duplicates": { - "type": - "string", - "description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. Remove duplicate snps, indels, both, all, exact matches, or none (old -D option)", - "help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).", - "enum": ["snps", "indels", "both", "all", "exact", "none"] - - - } - - - , - "fasta_ref": { - "type": - "string", - "description": "Type: `file`. Reference fasta sequence file", - "help_text": "Type: `file`. Reference fasta sequence file." - - } - - - , - "force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Try to proceed even if malformed tags are encountered", - "help_text": "Type: `boolean_true`, default: `false`. Try to proceed even if malformed tags are encountered. \nExperimental, use at your own risk.\n" - , - "default":false - } - - - , - "keep_sum": { - "type": - "string", - "description": "Type: `string`. Keep vector sum constant when splitting multiallelics (see github issue #360)", - "help_text": "Type: `string`. Keep vector sum constant when splitting multiallelics (see github issue #360).\n" - - } - - - , - "multiallelics": { - "type": - "string", - "description": "Type: `string`, choices: ``+snps`, `+indels`, `+both`, `+any`, `-snps`, `-indels`, `-both`, `-any``. Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both]", - "help_text": "Type: `string`, choices: ``+snps`, `+indels`, `+both`, `+any`, `-snps`, `-indels`, `-both`, `-any``. Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].\n", - "enum": ["+snps", "+indels", "+both", "+any", "-snps", "-indels", "-both", "-any"] - - - } - - - , - "no_version": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the header", - "help_text": "Type: `boolean_true`, default: `false`. Do not append version and command line information to the header." - , - "default":false - } - - - , - "do_not_normalize": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not normalize indels (with -m or -c s)", - "help_text": "Type: `boolean_true`, default: `false`. Do not normalize indels (with -m or -c s)." - , - "default":false - } - - - , - "output_type": { - "type": - "string", - "description": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "help_text": "Type: `string`, choices: ``u`, `z`, `b`, `v``. Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", - "enum": ["u", "z", "b", "v"] - - - } - - - , - "old_rec_tag": { - "type": - "string", - "description": "Type: `string`. Annotate modified records with INFO/STR indicating the original variant", - "help_text": "Type: `string`. Annotate modified records with INFO/STR indicating the original variant." - - } - - - , - "regions": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" - - } - - - , - "regions_file": { - "type": - "string", - "description": "Type: `file`. Restrict to regions listed in a file", - "help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n" - - } - - - , - "regions_overlap": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - - , - "site_win": { - "type": - "integer", - "description": "Type: `integer`. Buffer for sorting lines that changed position during realignment", - "help_text": "Type: `integer`. Buffer for sorting lines that changed position during realignment.\n" - - } - - - , - "strict_filter": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When merging (-m+), merged site is PASS only if all sites being merged PASS", - "help_text": "Type: `boolean_true`, default: `false`. When merging (-m+), merged site is PASS only if all sites being merged PASS." - , - "default":false - } - - - , - "targets": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Similar to --regions but streams rather than index-jumps", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Similar to --regions but streams rather than index-jumps." - - } - - - , - "targets_file": { - "type": - "string", - "description": "Type: `file`. Similar to --regions_file but streams rather than index-jumps", - "help_text": "Type: `file`. Similar to --regions_file but streams rather than index-jumps." - - } - - - , - "targets_overlap": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2)", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2).\nSimilar to --regions_overlap.\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcftools_norm", + "description": "Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; \nrecover multiallelics from multiple rows. \n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input VCF/BCF file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output normalized VCF/BCF file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "atomize": { + "type": "boolean", + "description": "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "atom_overlaps": { + "type": "string", + "description": "Use the star allele (*) for overlapping alleles or set to missing (.).\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``.`, `*``. ", + "enum": [ + ".", + "*" + ] + }, + "check_ref": { + "type": "string", + "description": "Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``e`, `w`, `x`, `s``. ", + "enum": [ + "e", + "w", + "x", + "s" + ] + }, + "remove_duplicates": { + "type": "string", + "description": "Remove duplicate snps, indels, both, all, exact matches, or none (old -D option).", + "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `exact`, `none``. ", + "enum": [ + "snps", + "indels", + "both", + "all", + "exact", + "none" + ] + }, + "fasta_ref": { + "type": "string", + "format": "path", + "description": "Reference fasta sequence file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "force": { + "type": "boolean", + "description": "Try to proceed even if malformed tags are encountered", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep_sum": { + "type": "string", + "description": "Keep vector sum constant when splitting multiallelics (see github issue #360).\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "multiallelics": { + "type": "string", + "description": "Split multiallelics (-) or join biallelics (+), type: snps, indels, both, any [default: both].\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``+snps`, `+indels`, `+both`, `+any`, `-snps`, `-indels`, `-both`, `-any``. ", + "enum": [ + "+snps", + "+indels", + "+both", + "+any", + "-snps", + "-indels", + "-both", + "-any" + ] + }, + "no_version": { + "type": "boolean", + "description": "Do not append version and command line information to the header.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "do_not_normalize": { + "type": "boolean", + "description": "Do not normalize indels (with -m or -c s).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_type": { + "type": "string", + "description": "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed BCF\n v: uncompressed VCF\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``u`, `z`, `b`, `v``. ", + "enum": [ + "u", + "z", + "b", + "v" + ] + }, + "old_rec_tag": { + "type": "string", + "description": "Annotate modified records with INFO/STR indicating the original variant.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "regions": { + "type": "string", + "description": "Restrict to comma-separated list of regions", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "regions_file": { + "type": "string", + "format": "path", + "description": "Restrict to regions listed in a file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "regions_overlap": { + "type": "string", + "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + }, + "site_win": { + "type": "integer", + "description": "Buffer for sorting lines that changed position during realignment.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "strict_filter": { + "type": "boolean", + "description": "When merging (-m+), merged site is PASS only if all sites being merged PASS.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "targets": { + "type": "string", + "description": "Similar to --regions but streams rather than index-jumps.", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "targets_file": { + "type": "string", + "format": "path", + "description": "Similar to --regions_file but streams rather than index-jumps.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "targets_overlap": { + "type": "string", + "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\nSimilar to --regions_overlap.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index 50430860..d97e24d6 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -188,9 +184,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -215,6 +211,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index fc010259..6b724ab6 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3278,9 +3271,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3296,6 +3289,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json index 46f051fd..e4c1303d 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json @@ -1,121 +1,80 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcftools_sort", -"description": "Sorts VCF/BCF files.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input VCF/BCF file", - "help_text": "Type: `file`, required. Input VCF/BCF file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output sorted VCF/BCF file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "output_type": { - "type": - "string", - "description": "Type: `string`, choices: ``b`, `u`, `z`, `v``. Compresses or uncompresses the output", - "help_text": "Type: `string`, choices: ``b`, `u`, `z`, `v``. Compresses or uncompresses the output.\nThe options are:\n b: compressed BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF. \n", - "enum": ["b", "u", "z", "v"] - - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcftools_sort", + "description": "Sorts VCF/BCF files.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input VCF/BCF file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output sorted VCF/BCF file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "output_type": { + "type": "string", + "description": "Compresses or uncompresses the output.\nThe options are:\n b: compressed BCF, \n u: uncompressed BCF, \n z: compressed VCF, \n v: uncompressed VCF", + "help_text": "Type: `string`, multiple: `False`, choices: ``b`, `u`, `z`, `v``. ", + "enum": [ + "b", + "u", + "z", + "v" + ] + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index c9ef6bc6..ff770179 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -10,10 +10,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -461,9 +457,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -488,6 +484,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index 0f650de8..3be52f71 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -3047,14 +3047,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3567,9 +3560,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_stats", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3585,6 +3578,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json index 168dea65..fbc5ccbf 100644 --- a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json @@ -1,338 +1,215 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcftools_stats", -"description": "Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats.\nWhen two files are given, the program generates separate stats for intersection\nand the complements. By default only sites are compared, -s/-S must given to include\nalso sample columns.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file", - "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Input VCF/BCF file. Maximum of two files." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output txt statistics file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output txt statistics file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "allele_frequency_bins": { - "type": - "string", - "description": "Type: `string`, example: `0.1,0.5,1`. Allele frequency bins, a list of bin values (0", - "help_text": "Type: `string`, example: `0.1,0.5,1`. Allele frequency bins, a list of bin values (0.1,0.5,1).\n" - - } - - - , - "allele_frequency_bins_file": { - "type": - "string", - "description": "Type: `file`. Same as allele_frequency_bins, but in a file", - "help_text": "Type: `file`. Same as allele_frequency_bins, but in a file.\nFormat of file is one value per line. \ne.g. \n 0.1\n 0.5\n 1\n" - - } - - - , - "allele_frequency_tag": { - "type": - "string", - "description": "Type: `string`. Allele frequency tag to use, by default estimated from AN,AC or GT", - "help_text": "Type: `string`. Allele frequency tag to use, by default estimated from AN,AC or GT.\n" - - } - - - , - "first_allele_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Include only 1st allele at multiallelic sites", - "help_text": "Type: `boolean_true`, default: `false`. Include only 1st allele at multiallelic sites.\n" - , - "default":false - } - - - , - "collapse": { - "type": - "string", - "description": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. Treat as identical records with \u003csnps|indels|both|all|some|none\u003e", - "help_text": "Type: `string`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. Treat as identical records with \u003csnps|indels|both|all|some|none\u003e.\nSee https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n", - "enum": ["snps", "indels", "both", "all", "some", "none"] - - - } - - - , - "depth": { - "type": - "string", - "description": "Type: `string`, example: `0,500,1`. Depth distribution: min,max,bin size", - "help_text": "Type: `string`, example: `0,500,1`. Depth distribution: min,max,bin size.\n" - - } - - - , - "exclude": { - "type": - "string", - "description": "Type: `string`, example: `QUAL \u003c 30 \u0026\u0026 DP \u003c 10`. Exclude sites for which the expression is true", - "help_text": "Type: `string`, example: `QUAL \u003c 30 \u0026\u0026 DP \u003c 10`. Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" - - } - - - , - "exons": { - "type": - "string", - "description": "Type: `file`. tab-delimited file with exons for indel frameshifts statistics", - "help_text": "Type: `file`. tab-delimited file with exons for indel frameshifts statistics. \nThe columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. \nThe file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2 -e3 file.gz).\n" - - } - - - , - "apply_filters": { - "type": - "string", - "description": "Type: `string`. Require at least one of the listed FILTER strings (e", - "help_text": "Type: `string`. Require at least one of the listed FILTER strings (e.g. \"PASS,.\").\n" - - } - - - , - "fasta_reference": { - "type": - "string", - "description": "Type: `file`. Faidx indexed reference sequence file to determine INDEL context", - "help_text": "Type: `file`. Faidx indexed reference sequence file to determine INDEL context.\n" - - } - - - , - "include": { - "type": - "string", - "description": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true", - "help_text": "Type: `string`, example: `QUAL \u003e= 30 \u0026\u0026 DP \u003e= 10`. Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n" - - } - - - , - "split_by_ID": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Collect stats for sites with ID separately (known vs novel)", - "help_text": "Type: `boolean_true`, default: `false`. Collect stats for sites with ID separately (known vs novel).\n" - , - "default":false - } - - - , - "regions": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Restrict to comma-separated list of regions. \nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" - - } - - - , - "regions_file": { - "type": - "string", - "description": "Type: `file`. Restrict to regions listed in a file", - "help_text": "Type: `file`. Restrict to regions listed in a file. \nRegions can be specified either on a VCF, BED, or tab-delimited file (the default). \nFor more information check manual.\n" - - } - - - , - "regions_overlap": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\")", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. This option controls how overlapping records are determined: \nset to \u0027pos\u0027 or \u00270\u0027 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to \u0027record\u0027 or \u00271\u0027 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to \u0027variant\u0027 or \u00272\u0027 to include only true overlapping variation (compare the full VCF representation \"TA\u003eT-\" vs the true sequence variation \"A\u003e-\").\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - - , - "samples": { - "type": - "string", - "description": "Type: `string`. List of samples for sample stats, \"-\" to include all samples", - "help_text": "Type: `string`. List of samples for sample stats, \"-\" to include all samples.\n" - - } - - - , - "samples_file": { - "type": - "string", - "description": "Type: `file`. File of samples to include", - "help_text": "Type: `file`. File of samples to include.\ne.g. \n sample1 1\n sample2 2\n sample3 2\n" - - } - - - , - "targets": { - "type": - "string", - "description": "Type: `string`, example: `20:1000000-2000000`. Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index", - "help_text": "Type: `string`, example: `20:1000000-2000000`. Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index. Both -r and -t options can be applied simultaneously: -r uses the \nindex to jump to a region and -t discards positions which are not in the targets. Unlike -r, targets \ncan be prefixed with \"^\" to request logical complement. For example, \"^X,Y,MT\" indicates that \nsequences X, Y and MT should be skipped. Yet another difference between the -t/-T and -r/-R is \nthat -r/-R checks for proper overlaps and considers both POS and the end position of an indel, \nwhile -t/-T considers the POS coordinate only (by default; see also --regions-overlap and --targets-overlap). \nNote that -t cannot be used in combination with -T.\nFollowing formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,\u2026\u200b].\n" - - } - - - , - "targets_file": { - "type": - "string", - "description": "Type: `file`. Similar to --regions_file option but streams rather than index-jumps", - "help_text": "Type: `file`. Similar to --regions_file option but streams rather than index-jumps.\n" - - } - - - , - "targets_overlaps": { - "type": - "string", - "description": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2)", - "help_text": "Type: `string`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n", - "enum": ["pos", "record", "variant", "0", "1", "2"] - - - } - - - , - "user_tstv": { - "type": - "string", - "description": "Type: `string`. Collect Ts/Tv stats for any tag using the given binning [0:1:100]", - "help_text": "Type: `string`. Collect Ts/Tv stats for any tag using the given binning [0:1:100].\nFormat is \u003cTAG[:min:max:n]\u003e.\nA subfield can be selected as e.g. \u0027PV4[0]\u0027, here the first value of the PV4 tag.\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Produce verbose per-site and per-sample output", - "help_text": "Type: `boolean_true`, default: `false`. Produce verbose per-site and per-sample output.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcftools_stats", + "description": "Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats.\nWhen two files are given, the program generates separate stats for intersection\nand the complements. By default only sites are compared, -s/-S must given to include\nalso sample columns.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Input VCF/BCF file", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output txt statistics file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "allele_frequency_bins": { + "type": "string", + "description": "Allele frequency bins, a list of bin values (0.1,0.5,1).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"0.1,0.5,1\"`. " + }, + "allele_frequency_bins_file": { + "type": "string", + "format": "path", + "description": "Same as allele_frequency_bins, but in a file.\nFormat of file is one value per line", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "allele_frequency_tag": { + "type": "string", + "description": "Allele frequency tag to use, by default estimated from AN,AC or GT.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "first_allele_only": { + "type": "boolean", + "description": "Include only 1st allele at multiallelic sites.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "collapse": { + "type": "string", + "description": "Treat as identical records with .\nSee https://samtools.github.io/bcftools/bcftools.html#common_options for details.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``snps`, `indels`, `both`, `all`, `some`, `none``. ", + "enum": [ + "snps", + "indels", + "both", + "all", + "some", + "none" + ] + }, + "depth": { + "type": "string", + "description": "Depth distribution: min,max,bin size.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"0,500,1\"`. " + }, + "exclude": { + "type": "string", + "description": "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL < 30 && DP < 10\"`. " + }, + "exons": { + "type": "string", + "format": "path", + "description": "tab-delimited file with exons for indel frameshifts statistics", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "apply_filters": { + "type": "string", + "description": "Require at least one of the listed FILTER strings (e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "fasta_reference": { + "type": "string", + "format": "path", + "description": "Faidx indexed reference sequence file to determine INDEL context.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "include": { + "type": "string", + "description": "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions for details.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"QUAL >= 30 && DP >= 10\"`. " + }, + "split_by_ID": { + "type": "boolean", + "description": "Collect stats for sites with ID separately (known vs novel).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "regions": { + "type": "string", + "description": "Restrict to comma-separated list of regions", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "regions_file": { + "type": "string", + "format": "path", + "description": "Restrict to regions listed in a file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "regions_overlap": { + "type": "string", + "description": "This option controls how overlapping records are determined: \nset to 'pos' or '0' if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, \nand includes indels with POS at the end of a region, which are technically outside the region); \nor set to 'variant' or '2' to include only true overlapping variation (compare the full VCF representation \"TA>T-\" vs the true sequence variation \"A>-\").\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + }, + "samples": { + "type": "string", + "description": "List of samples for sample stats, \"-\" to include all samples.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "samples_file": { + "type": "string", + "format": "path", + "description": "File of samples to include.\ne.g", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "targets": { + "type": "string", + "description": "Similar as -r, --regions, but the next position is accessed by streaming the whole VCF/BCF \nrather than using the tbi/csi index", + "help_text": "Type: `string`, multiple: `False`, example: `\"20:1000000-2000000\"`. " + }, + "targets_file": { + "type": "string", + "format": "path", + "description": "Similar to --regions_file option but streams rather than index-jumps.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "targets_overlaps": { + "type": "string", + "description": "Include if POS in the region (0), record overlaps (1), variant overlaps (2).\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``pos`, `record`, `variant`, `0`, `1`, `2``. ", + "enum": [ + "pos", + "record", + "variant", + "0", + "1", + "2" + ] + }, + "user_tstv": { + "type": "string", + "description": "Collect Ts/Tv stats for any tag using the given binning [0:1:100].\nFormat is .\nA subfield can be selected as e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "verbose": { + "type": "boolean", + "description": "Produce verbose per-site and per-sample output.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index c6ca32b9..44288afb 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -431,9 +431,9 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -458,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index f8910fd5..02f26285 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3571,9 +3571,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3589,6 +3589,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bcl_convert/nextflow_schema.json b/target/nextflow/bcl_convert/nextflow_schema.json index 9927d09d..5fc9ccb2 100644 --- a/target/nextflow/bcl_convert/nextflow_schema.json +++ b/target/nextflow/bcl_convert/nextflow_schema.json @@ -1,359 +1,205 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bcl_convert", -"description": "Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n", -"type": "object", -"definitions": { - - - - "input arguments" : { - "title": "Input arguments", - "type": "object", - "description": "No description", - "properties": { - - - "bcl_input_directory": { - "type": - "string", - "description": "Type: `file`, required, example: `bcl_dir`. Input run directory", - "help_text": "Type: `file`, required, example: `bcl_dir`. Input run directory" - - } - - - , - "sample_sheet": { - "type": - "string", - "description": "Type: `file`, example: `bcl_dir/sample_sheet.csv`. Path to SampleSheet", - "help_text": "Type: `file`, example: `bcl_dir/sample_sheet.csv`. Path to SampleSheet.csv file (default searched for in --bcl_input_directory)" - - } - - - , - "run_info": { - "type": - "string", - "description": "Type: `file`, example: `bcl_dir/RunInfo.xml`. Path to RunInfo", - "help_text": "Type: `file`, example: `bcl_dir/RunInfo.xml`. Path to RunInfo.xml file (default root of BCL input directory)" - - } - - -} -}, - - - "lane and tile settings" : { - "title": "Lane and tile settings", - "type": "object", - "description": "No description", - "properties": { - - - "bcl_only_lane": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Convert only specified lane number (default all lanes)", - "help_text": "Type: `integer`, example: `1`. Convert only specified lane number (default all lanes)" - - } - - - , - "first_tile_only": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Only convert first tile of input (for testing \u0026 debugging)", - "help_text": "Type: `boolean`, example: `true`. Only convert first tile of input (for testing \u0026 debugging)" - - } - - - , - "tiles": { - "type": - "string", - "description": "Type: `string`, example: `s_[0-9]+_1`. Process only a subset of tiles by a regular expression", - "help_text": "Type: `string`, example: `s_[0-9]+_1`. Process only a subset of tiles by a regular expression" - - } - - - , - "exclude_tiles": { - "type": - "string", - "description": "Type: `string`, example: `s_[0-9]+_1`. Exclude set of tiles by a regular expression", - "help_text": "Type: `string`, example: `s_[0-9]+_1`. Exclude set of tiles by a regular expression" - - } - - -} -}, - - - "resource arguments" : { - "title": "Resource arguments", - "type": "object", - "description": "No description", - "properties": { - - - "shared_thread_odirect_output": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Use linux native asynchronous io (io_submit) for file output (Default=false)", - "help_text": "Type: `boolean`, example: `true`. Use linux native asynchronous io (io_submit) for file output (Default=false)" - - } - - - , - "bcl_num_parallel_tiles": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. \\# of tiles to process in parallel (default 1)", - "help_text": "Type: `integer`, example: `1`. \\# of tiles to process in parallel (default 1)" - - } - - - , - "bcl_num_conversion_threads": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. \\# of threads for conversion (per tile, default # cpu threads)", - "help_text": "Type: `integer`, example: `1`. \\# of threads for conversion (per tile, default # cpu threads)" - - } - - - , - "bcl_num_compression_threads": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. \\# of threads for fastq", - "help_text": "Type: `integer`, example: `1`. \\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)" - - } - - - , - "bcl_num_decompression_threads": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. \\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8)", - "help_text": "Type: `integer`, example: `1`. \\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8). Only applies when preloading files" - - } - - -} -}, - - - "run arguments" : { - "title": "Run arguments", - "type": "object", - "description": "No description", - "properties": { - - - "bcl_only_matched_reads": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. For pure BCL conversion, do not output files for \u0027Undetermined\u0027 [unmatched] reads (output by default)", - "help_text": "Type: `boolean`, example: `true`. For pure BCL conversion, do not output files for \u0027Undetermined\u0027 [unmatched] reads (output by default)" - - } - - - , - "no_lane_splitting": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Do not split FASTQ file by lane (false by default)", - "help_text": "Type: `boolean`, example: `true`. Do not split FASTQ file by lane (false by default)" - - } - - - , - "num_unknown_barcodes_reported": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. \\# of Top Unknown Barcodes to output (1000 by default)", - "help_text": "Type: `integer`, example: `1000`. \\# of Top Unknown Barcodes to output (1000 by default)" - - } - - - , - "bcl_validate_sample_sheet_only": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Only validate RunInfo", - "help_text": "Type: `boolean`, example: `true`. Only validate RunInfo.xml \u0026 SampleSheet files (produce no FASTQ files)" - - } - - - , - "strict_mode": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Abort if any files are missing (false by default)", - "help_text": "Type: `boolean`, example: `true`. Abort if any files are missing (false by default)" - - } - - - , - "sample_name_column_enabled": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Use sample sheet \u0027Sample_Name\u0027 column when naming fastq files \u0026 subdirectories", - "help_text": "Type: `boolean`, example: `true`. Use sample sheet \u0027Sample_Name\u0027 column when naming fastq files \u0026 subdirectories" - - } - - -} -}, - - - "output arguments" : { - "title": "Output arguments", - "type": "object", - "description": "No description", - "properties": { - - - "output_directory": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Output directory containig fastq files", - "help_text": "Type: `file`, required, default: `$id.$key.output_directory`, example: `fastq_dir`. Output directory containig fastq files" - , - "default":"$id.$key.output_directory" - } - - - , - "bcl_sampleproject_subdirectories": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Output to subdirectories based upon sample sheet \u0027Sample_Project\u0027 column", - "help_text": "Type: `boolean`, example: `true`. Output to subdirectories based upon sample sheet \u0027Sample_Project\u0027 column" - - } - - - , - "fastq_gzip_compression_level": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Set fastq output compression level 0-9 (default 1)", - "help_text": "Type: `integer`, example: `1`. Set fastq output compression level 0-9 (default 1)" - - } - - - , - "reports": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.reports`, example: `reports_dir`. Reports directory", - "help_text": "Type: `file`, default: `$id.$key.reports`, example: `reports_dir`. Reports directory" - , - "default":"$id.$key.reports" - } - - - , - "logs": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Reports directory", - "help_text": "Type: `file`, default: `$id.$key.logs`, example: `logs_dir`. Reports directory" - , - "default":"$id.$key.logs" - } - - - , - "force": { - "type": - "boolean", - "description": "Type: `boolean`, example: `true`. Allow destination directory to already exist and overwrite files", - "help_text": "Type: `boolean`, example: `true`. Allow destination directory to already exist and overwrite files.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bcl_convert", + "description": "Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n", + "type": "object", + "$defs": { + "input arguments": { + "title": "Input arguments", + "type": "object", + "description": "No description", + "properties": { + "bcl_input_directory": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input run directory", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"bcl_dir\"`. " + }, + "sample_sheet": { + "type": "string", + "format": "path", + "description": "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"bcl_dir/sample_sheet.csv\"`. " + }, + "run_info": { + "type": "string", + "format": "path", + "description": "Path to RunInfo.xml file (default root of BCL input directory)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"bcl_dir/RunInfo.xml\"`. " + } + } }, - - { - "$ref": "#/definitions/lane and tile settings" + "lane and tile settings": { + "title": "Lane and tile settings", + "type": "object", + "description": "No description", + "properties": { + "bcl_only_lane": { + "type": "integer", + "description": "Convert only specified lane number (default all lanes)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "first_tile_only": { + "type": "boolean", + "description": "Only convert first tile of input (for testing & debugging)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "tiles": { + "type": "string", + "description": "Process only a subset of tiles by a regular expression", + "help_text": "Type: `string`, multiple: `False`, example: `\"s_[0-9]+_1\"`. " + }, + "exclude_tiles": { + "type": "string", + "description": "Exclude set of tiles by a regular expression", + "help_text": "Type: `string`, multiple: `False`, example: `\"s_[0-9]+_1\"`. " + } + } }, - - { - "$ref": "#/definitions/resource arguments" + "resource arguments": { + "title": "Resource arguments", + "type": "object", + "description": "No description", + "properties": { + "shared_thread_odirect_output": { + "type": "boolean", + "description": "Use linux native asynchronous io (io_submit) for file output (Default=false)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "bcl_num_parallel_tiles": { + "type": "integer", + "description": "\\# of tiles to process in parallel (default 1)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "bcl_num_conversion_threads": { + "type": "integer", + "description": "\\# of threads for conversion (per tile, default # cpu threads)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "bcl_num_compression_threads": { + "type": "integer", + "description": "\\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "bcl_num_decompression_threads": { + "type": "integer", + "description": "\\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + } + } }, - - { - "$ref": "#/definitions/run arguments" + "run arguments": { + "title": "Run arguments", + "type": "object", + "description": "No description", + "properties": { + "bcl_only_matched_reads": { + "type": "boolean", + "description": "For pure BCL conversion, do not output files for 'Undetermined' [unmatched] reads (output by default)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "no_lane_splitting": { + "type": "boolean", + "description": "Do not split FASTQ file by lane (false by default)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "num_unknown_barcodes_reported": { + "type": "integer", + "description": "\\# of Top Unknown Barcodes to output (1000 by default)", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "bcl_validate_sample_sheet_only": { + "type": "boolean", + "description": "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "strict_mode": { + "type": "boolean", + "description": "Abort if any files are missing (false by default)", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "sample_name_column_enabled": { + "type": "boolean", + "description": "Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + } + } }, - - { - "$ref": "#/definitions/output arguments" + "output arguments": { + "title": "Output arguments", + "type": "object", + "description": "No description", + "properties": { + "output_directory": { + "type": "string", + "format": "path", + "description": "Output directory containig fastq files", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_directory\"`, direction: `output`, example: `\"fastq_dir\"`. ", + "default": "$id.$key.output_directory" + }, + "bcl_sampleproject_subdirectories": { + "type": "boolean", + "description": "Output to subdirectories based upon sample sheet 'Sample_Project' column", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + }, + "fastq_gzip_compression_level": { + "type": "integer", + "description": "Set fastq output compression level 0-9 (default 1)", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "reports": { + "type": "string", + "format": "path", + "description": "Reports directory", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.reports\"`, direction: `output`, example: `\"reports_dir\"`. ", + "default": "$id.$key.reports" + }, + "logs": { + "type": "string", + "format": "path", + "description": "Reports directory", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.logs\"`, direction: `output`, example: `\"logs_dir\"`. ", + "default": "$id.$key.logs" + }, + "force": { + "type": "boolean", + "description": "Allow destination directory to already exist and overwrite files.\n", + "help_text": "Type: `boolean`, multiple: `False`, example: `true`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input arguments" + }, + { + "$ref": "#/$defs/lane and tile settings" + }, + { + "$ref": "#/$defs/resource arguments" + }, + { + "$ref": "#/$defs/run arguments" + }, + { + "$ref": "#/$defs/output arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml index fcf03bb0..d038d27d 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml @@ -23,6 +23,8 @@ authors: roles: - "contributor" info: + links: + linkedin: "weiwei-schultz" organizations: - name: "Janssen R&D US" role: "Associate Director Data Sciences" @@ -277,9 +279,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -304,6 +306,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf index 0307808a..9db83a74 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3071,6 +3071,9 @@ meta = [ "contributor" ], "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, "organizations" : [ { "name" : "Janssen R&D US", @@ -3376,9 +3379,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3394,6 +3397,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow_schema.json b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow_schema.json index 946d186c..e69de29b 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow_schema.json +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/nextflow_schema.json @@ -1,172 +0,0 @@ -{ -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bd_rhapsody_make_reference", -"description": "The Reference Files Generator creates an archive containing Genome Index\nand Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis Pipeline. The app takes as input one or more FASTA and GTF files\nand produces a compressed archive in the form of a tar.gz file. The \narchive contains:\n\n- STAR index\n- Filtered GTF file\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "genome_fasta": { - "type": - "string", - "description": "Type: List of `file`, required, example: `genome_sequence.fa.gz`, multiple_sep: `\";\"`. Reference genome file in FASTA or FASTA", - "help_text": "Type: List of `file`, required, example: `genome_sequence.fa.gz`, multiple_sep: `\";\"`. Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse." - - } - - - , - "gtf": { - "type": - "string", - "description": "Type: List of `file`, required, example: `transcriptome_annotation.gtf.gz`, multiple_sep: `\";\"`. File path to the transcript annotation files in GTF or GTF", - "help_text": "Type: List of `file`, required, example: `transcriptome_annotation.gtf.gz`, multiple_sep: `\";\"`. File path to the transcript annotation files in GTF or GTF.GZ format. The Sequence Analysis Pipeline requires the \u0027gene_name\u0027 or \n\u0027gene_id\u0027 attribute to be set on each gene and exon feature. Gene and exon feature lines must have the same attribute, and exons\nmust have a corresponding gene with the same value. For TCR/BCR assays, the TCR or BCR gene segments must have the \u0027gene_type\u0027 or\n\u0027gene_biotype\u0027 attribute set, and the value should begin with \u0027TR\u0027 or \u0027IG\u0027, respectively.\n" - - } - - - , - "extra_sequences": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. File path to additional sequences in FASTA format to use when building the STAR index", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. File path to additional sequences in FASTA format to use when building the STAR index. (e.g. transgenes or CRISPR guide barcodes).\nGTF lines for these sequences will be automatically generated and combined with the main GTF.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "reference_archive": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.reference_archive.gz`, example: `star_index.tar.gz`. A Compressed archive containing the Reference Genome Index and annotation GTF files", - "help_text": "Type: `file`, required, default: `$id.$key.reference_archive.gz`, example: `star_index.tar.gz`. A Compressed archive containing the Reference Genome Index and annotation GTF files. This archive is meant to be used as an\ninput in the BD Rhapsody Sequencing Analysis Pipeline.\n" - , - "default":"$id.$key.reference_archive.gz" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "mitochondrial_contigs": { - "type": - "string", - "description": "Type: List of `string`, default: `chrM;chrMT;M;MT`, multiple_sep: `\";\"`. Names of the Mitochondrial contigs in the provided Reference Genome", - "help_text": "Type: List of `string`, default: `chrM;chrMT;M;MT`, multiple_sep: `\";\"`. Names of the Mitochondrial contigs in the provided Reference Genome. Fragments originating from contigs other than these are\nidentified as \u0027nuclear fragments\u0027 in the ATACseq analysis pipeline.\n" - , - "default":"chrM;chrMT;M;MT" - } - - - , - "filtering_off": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute", - "help_text": "Type: `boolean_true`, default: `false`. By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute. Only features \nhaving the following attribute values are kept:\n\n - protein_coding\n - lncRNA (lincRNA and antisense for Gencode \u003c v31/M22/Ensembl97)\n - IG_LV_gene\n - IG_V_gene\n - IG_V_pseudogene\n - IG_D_gene\n - IG_J_gene\n - IG_J_pseudogene\n - IG_C_gene\n - IG_C_pseudogene\n - TR_V_gene\n - TR_V_pseudogene\n - TR_D_gene\n - TR_J_gene\n - TR_J_pseudogene\n - TR_C_gene\n\n If you have already pre-filtered the input Annotation files and/or wish to turn-off the filtering, please set this option to True.\n" - , - "default":false - } - - - , - "wta_only_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build a WTA only index, otherwise builds a WTA + ATAC index", - "help_text": "Type: `boolean_true`, default: `false`. Build a WTA only index, otherwise builds a WTA + ATAC index." - , - "default":false - } - - - , - "extra_star_params": { - "type": - "string", - "description": "Type: `string`, example: `--limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11`. Additional parameters to pass to STAR when building the genome index", - "help_text": "Type: `string`, example: `--limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11`. Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" - }, - - { - "$ref": "#/definitions/outputs" - }, - - { - "$ref": "#/definitions/arguments" - }, - - { - "$ref": "#/definitions/nextflow input-output arguments" - } -] -} diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml index 3cdd59ed..8d6d8ffb 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml @@ -23,6 +23,8 @@ authors: roles: - "contributor" info: + links: + linkedin: "weiwei-schultz" organizations: - name: "Janssen R&D US" role: "Associate Director Data Sciences" @@ -1118,9 +1120,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1145,6 +1147,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf index 5151152b..fd38b464 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf @@ -3071,6 +3071,9 @@ meta = [ "contributor" ], "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, "organizations" : [ { "name" : "Janssen R&D US", @@ -4423,9 +4426,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -4441,6 +4444,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json index cbff45df..5fd180ee 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/nextflow_schema.json @@ -1,971 +1,645 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bd_rhapsody_sequence_analysis", -"description": "BD Rhapsody Sequence Analysis CWL pipeline v2.2.\n\nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody\u2122 assay kits, including: Whole Transcriptome\nmRNA (WTA), Targeted mRNA, AbSeq Antibody-Oligonucleotides (ABC), Single-Cell Multiplexing (SMK),\nTCR/BCR (VDJ), and ATAC-Seq.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "reads": { - "type": - "string", - "description": "Type: List of `file`, example: `WTALibrary_S1_L001_R1_001.fastq.gz;WTALibrary_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. Reads (optional) - Path to your FASTQ", - "help_text": "Type: List of `file`, example: `WTALibrary_S1_L001_R1_001.fastq.gz;WTALibrary_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. Reads (optional) - Path to your FASTQ.GZ formatted read files from libraries that may include:\n\n- WTA mRNA\n- Targeted mRNA\n- AbSeq\n- Sample Multiplexing\n- VDJ\n\nYou may specify as many R1/R2 read pairs as you want.\n" - - } - - - , - "reads_atac": { - "type": - "string", - "description": "Type: List of `file`, example: `ATACLibrary_S2_L001_R1_001.fastq.gz;ATACLibrary_S2_L001_R2_001.fastq.gz;ATACLibrary_S2_L001_I2_001.fastq.gz`, multiple_sep: `\";\"`. Path to your FASTQ", - "help_text": "Type: List of `file`, example: `ATACLibrary_S2_L001_R1_001.fastq.gz;ATACLibrary_S2_L001_R2_001.fastq.gz;ATACLibrary_S2_L001_I2_001.fastq.gz`, multiple_sep: `\";\"`. Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.\nYou may specify as many R1/R2/I2 files as you want.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "Outputs for all pipeline runs", - "properties": { - - - "output_dir": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline", - "help_text": "Type: `file`, required, default: `$id.$key.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline." - , - "default":"$id.$key.output_dir" - } - - - , - "output_seurat": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_seurat.rds`, example: `output_seurat.rds`. Single-cell analysis tool inputs", - "help_text": "Type: `file`, default: `$id.$key.output_seurat.rds`, example: `output_seurat.rds`. Single-cell analysis tool inputs. Seurat (.rds) input file containing RSEC molecules data table and all cell annotation metadata." - , - "default":"$id.$key.output_seurat.rds" - } - - - , - "output_mudata": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_mudata.h5mu`, example: `output_mudata.h5mu`. Single-cell analysis tool inputs", - "help_text": "Type: `file`, default: `$id.$key.output_mudata.h5mu`, example: `output_mudata.h5mu`. Single-cell analysis tool inputs. Scanpy / Muon input file containing RSEC molecules data table and all cell annotation metadata." - , - "default":"$id.$key.output_mudata.h5mu" - } - - - , - "metrics_summary": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.metrics_summary.csv`, example: `metrics_summary.csv`. Metrics Summary", - "help_text": "Type: `file`, default: `$id.$key.metrics_summary.csv`, example: `metrics_summary.csv`. Metrics Summary. Report containing sequencing, molecules, and cell metrics." - , - "default":"$id.$key.metrics_summary.csv" - } - - - , - "pipeline_report": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.pipeline_report.html`, example: `pipeline_report.html`. Pipeline Report", - "help_text": "Type: `file`, default: `$id.$key.pipeline_report.html`, example: `pipeline_report.html`. Pipeline Report. Summary report containing the results from the sequencing analysis pipeline run." - , - "default":"$id.$key.pipeline_report.html" - } - - - , - "rsec_mols_per_cell": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.rsec_mols_per_cell.zip`, example: `RSEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on RSEC", - "help_text": "Type: `file`, default: `$id.$key.rsec_mols_per_cell.zip`, example: `RSEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on RSEC" - , - "default":"$id.$key.rsec_mols_per_cell.zip" - } - - - , - "dbec_mols_per_cell": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dbec_mols_per_cell.zip`, example: `DBEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on DBEC", - "help_text": "Type: `file`, default: `$id.$key.dbec_mols_per_cell.zip`, example: `DBEC_MolsPerCell_MEX.zip`. Molecules per bioproduct per cell bassed on DBEC. DBEC data table is only output if the experiment includes targeted mRNA or AbSeq bioproducts." - , - "default":"$id.$key.dbec_mols_per_cell.zip" - } - - - , - "rsec_mols_per_cell_unfiltered": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.rsec_mols_per_cell_unfiltered.zip`, example: `RSEC_MolsPerCell_Unfiltered_MEX.zip`. Unfiltered tables containing all cell labels with \u226510 reads", - "help_text": "Type: `file`, default: `$id.$key.rsec_mols_per_cell_unfiltered.zip`, example: `RSEC_MolsPerCell_Unfiltered_MEX.zip`. Unfiltered tables containing all cell labels with \u226510 reads." - , - "default":"$id.$key.rsec_mols_per_cell_unfiltered.zip" - } - - - , - "bam": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bam.bam`, example: `BioProduct.bam`. Alignment file of R2 with associated R1 annotations for Bioproduct", - "help_text": "Type: `file`, default: `$id.$key.bam.bam`, example: `BioProduct.bam`. Alignment file of R2 with associated R1 annotations for Bioproduct." - , - "default":"$id.$key.bam.bam" - } - - - , - "bam_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bam_index.bai`, example: `BioProduct.bam.bai`. Index file for the alignment file", - "help_text": "Type: `file`, default: `$id.$key.bam_index.bai`, example: `BioProduct.bam.bai`. Index file for the alignment file." - , - "default":"$id.$key.bam_index.bai" - } - - - , - "bioproduct_stats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bioproduct_stats.csv`, example: `Bioproduct_Stats.csv`. Bioproduct Stats", - "help_text": "Type: `file`, default: `$id.$key.bioproduct_stats.csv`, example: `Bioproduct_Stats.csv`. Bioproduct Stats. Metrics from RSEC and DBEC Unique Molecular Identifier adjustment algorithms on a per-bioproduct basis." - , - "default":"$id.$key.bioproduct_stats.csv" - } - - - , - "dimred_tsne": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dimred_tsne.csv`, example: `tSNE_coordinates.csv`. t-SNE dimensionality reduction coordinates per cell index", - "help_text": "Type: `file`, default: `$id.$key.dimred_tsne.csv`, example: `tSNE_coordinates.csv`. t-SNE dimensionality reduction coordinates per cell index" - , - "default":"$id.$key.dimred_tsne.csv" - } - - - , - "dimred_umap": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.dimred_umap.csv`, example: `UMAP_coordinates.csv`. UMAP dimensionality reduction coordinates per cell index", - "help_text": "Type: `file`, default: `$id.$key.dimred_umap.csv`, example: `UMAP_coordinates.csv`. UMAP dimensionality reduction coordinates per cell index" - , - "default":"$id.$key.dimred_umap.csv" - } - - - , - "immune_cell_classification": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.immune_cell_classification.csv`, example: `Immune_Cell_Classification.csv`. Immune Cell Classification", - "help_text": "Type: `file`, default: `$id.$key.immune_cell_classification.csv`, example: `Immune_Cell_Classification.csv`. Immune Cell Classification. Cell type classification based on the expression of immune cell markers." - , - "default":"$id.$key.immune_cell_classification.csv" - } - - -} -}, - - - "references" : { - "title": "References", - "type": "object", - "description": "Assay type will be inferred from the provided reference(s).\nDo not provide both reference_archive and targeted_reference at the same time.\n\nValid reference input combinations:\n - reference_archive: WTA only\n - reference_archive \u0026 abseq_reference: WTA + AbSeq\n - reference_archive \u0026 supplemental_reference: WTA + extra transgenes\n - reference_archive \u0026 abseq_reference \u0026 supplemental_reference: WTA + AbSeq + extra transgenes\n - reference_archive: WTA + ATAC or ATAC only\n - reference_archive \u0026 supplemental_reference: WTA + ATAC + extra transgenes\n - targeted_reference: Targeted only\n - targeted_reference \u0026 abseq_reference: Targeted + AbSeq\n - abseq_reference: AbSeq only\n\nThe reference_archive can be generated with the bd_rhapsody_make_reference component.\nAlternatively, BD also provides standard references which can be downloaded from these locations:\n\n - Human: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Human_WTA_2023-02.tar.gz\n - Mouse: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Mouse_WTA_2023-02.tar.gz\n", - "properties": { - - - "reference_archive": { - "type": - "string", - "description": "Type: `file`, example: `RhapRef_Human_WTA_2023-02.tar.gz`. Path to Rhapsody WTA Reference in the tar", - "help_text": "Type: `file`, example: `RhapRef_Human_WTA_2023-02.tar.gz`. Path to Rhapsody WTA Reference in the tar.gz format.\n\nStructure of the reference archive:\n\n- `BD_Rhapsody_Reference_Files/`: top level folder\n - `star_index/`: sub-folder containing STAR index, that is files created with `STAR --runMode genomeGenerate`\n - GTF for gene-transcript-annotation e.g. \"gencode.v43.primary_assembly.annotation.gtf\"\n" - - } - - - , - "targeted_reference": { - "type": - "string", - "description": "Type: List of `file`, example: `BD_Rhapsody_Immune_Response_Panel_Hs.fasta`, multiple_sep: `\";\"`. Path to the targeted reference file in FASTA format", - "help_text": "Type: List of `file`, example: `BD_Rhapsody_Immune_Response_Panel_Hs.fasta`, multiple_sep: `\";\"`. Path to the targeted reference file in FASTA format.\n" - - } - - - , - "abseq_reference": { - "type": - "string", - "description": "Type: List of `file`, example: `AbSeq_reference.fasta`, multiple_sep: `\";\"`. Path to the AbSeq reference file in FASTA format", - "help_text": "Type: List of `file`, example: `AbSeq_reference.fasta`, multiple_sep: `\";\"`. Path to the AbSeq reference file in FASTA format. Only needed if BD AbSeq Ab-Oligos are used." - - } - - - , - "supplemental_reference": { - "type": - "string", - "description": "Type: List of `file`, example: `supplemental_reference.fasta`, multiple_sep: `\";\"`. Path to the supplemental reference file in FASTA format", - "help_text": "Type: List of `file`, example: `supplemental_reference.fasta`, multiple_sep: `\";\"`. Path to the supplemental reference file in FASTA format. Only needed if there are additional transgene sequences to be aligned against in a WTA assay experiment." - - } - - -} -}, - - - "multiplex outputs" : { - "title": "Multiplex outputs", - "type": "object", - "description": "Outputs when multiplex option is selected", - "properties": { - - - "sample_tag_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sample_tag_metrics.csv`, example: `Sample_Tag_Metrics.csv`. Sample Tag Metrics", - "help_text": "Type: `file`, default: `$id.$key.sample_tag_metrics.csv`, example: `Sample_Tag_Metrics.csv`. Sample Tag Metrics. Metrics from the sample determination algorithm." - , - "default":"$id.$key.sample_tag_metrics.csv" - } - - - , - "sample_tag_calls": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sample_tag_calls.csv`, example: `Sample_Tag_Calls.csv`. Sample Tag Calls", - "help_text": "Type: `file`, default: `$id.$key.sample_tag_calls.csv`, example: `Sample_Tag_Calls.csv`. Sample Tag Calls. Assigned Sample Tag for each putative cell" - , - "default":"$id.$key.sample_tag_calls.csv" - } - - - , - "sample_tag_counts": { - "type": - "string", - "description": "Type: List of `file`, default: `$id.$key.sample_tag_counts_*.zip`, example: `Sample_Tag1.zip`, multiple_sep: `\";\"`. Sample Tag Counts", - "help_text": "Type: List of `file`, default: `$id.$key.sample_tag_counts_*.zip`, example: `Sample_Tag1.zip`, multiple_sep: `\";\"`. Sample Tag Counts. Separate data tables and metric summary for cells assigned to each sample tag. Note: For putative cells that could not be assigned a specific Sample Tag, a Multiplet_and_Undetermined.zip file is also output." - , - "default":"$id.$key.sample_tag_counts_*.zip" - } - - - , - "sample_tag_counts_unassigned": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sample_tag_counts_unassigned.zip`, example: `Multiplet_and_Undetermined.zip`. Sample Tag Counts Unassigned", - "help_text": "Type: `file`, default: `$id.$key.sample_tag_counts_unassigned.zip`, example: `Multiplet_and_Undetermined.zip`. Sample Tag Counts Unassigned. Data table and metric summary for cells that could not be assigned a specific Sample Tag." - , - "default":"$id.$key.sample_tag_counts_unassigned.zip" - } - - -} -}, - - - "vdj outputs" : { - "title": "VDJ Outputs", - "type": "object", - "description": "Outputs when VDJ option selected", - "properties": { - - - "vdj_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.vdj_metrics.csv`, example: `VDJ_Metrics.csv`. VDJ Metrics", - "help_text": "Type: `file`, default: `$id.$key.vdj_metrics.csv`, example: `VDJ_Metrics.csv`. VDJ Metrics. Overall metrics from the VDJ analysis." - , - "default":"$id.$key.vdj_metrics.csv" - } - - - , - "vdj_per_cell": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.vdj_per_cell.csv`, example: `VDJ_perCell.csv`. VDJ Per Cell", - "help_text": "Type: `file`, default: `$id.$key.vdj_per_cell.csv`, example: `VDJ_perCell.csv`. VDJ Per Cell. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type." - , - "default":"$id.$key.vdj_per_cell.csv" - } - - - , - "vdj_per_cell_uncorrected": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.vdj_per_cell_uncorrected.csv`, example: `VDJ_perCell_uncorrected.csv`. VDJ Per Cell Uncorrected", - "help_text": "Type: `file`, default: `$id.$key.vdj_per_cell_uncorrected.csv`, example: `VDJ_perCell_uncorrected.csv`. VDJ Per Cell Uncorrected. Cell specific read and molecule counts, VDJ gene segments, CDR3 sequences, paired chains, and cell type." - , - "default":"$id.$key.vdj_per_cell_uncorrected.csv" - } - - - , - "vdj_dominant_contigs": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.vdj_dominant_contigs.csv`, example: `VDJ_Dominant_Contigs_AIRR.csv`. VDJ Dominant Contigs", - "help_text": "Type: `file`, default: `$id.$key.vdj_dominant_contigs.csv`, example: `VDJ_Dominant_Contigs_AIRR.csv`. VDJ Dominant Contigs. Dominant contig for each cell label chain type combination (putative cells only)." - , - "default":"$id.$key.vdj_dominant_contigs.csv" - } - - - , - "vdj_unfiltered_contigs": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.vdj_unfiltered_contigs.csv`, example: `VDJ_Unfiltered_Contigs_AIRR.csv`. VDJ Unfiltered Contigs", - "help_text": "Type: `file`, default: `$id.$key.vdj_unfiltered_contigs.csv`, example: `VDJ_Unfiltered_Contigs_AIRR.csv`. VDJ Unfiltered Contigs. All contigs that were assembled and annotated successfully (all cells)." - , - "default":"$id.$key.vdj_unfiltered_contigs.csv" - } - - -} -}, - - - "atac-seq outputs" : { - "title": "ATAC-Seq outputs", - "type": "object", - "description": "Outputs when ATAC-Seq option selected", - "properties": { - - - "atac_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_metrics.csv`, example: `ATAC_Metrics.csv`. ATAC Metrics", - "help_text": "Type: `file`, default: `$id.$key.atac_metrics.csv`, example: `ATAC_Metrics.csv`. ATAC Metrics. Overall metrics from the ATAC-Seq analysis." - , - "default":"$id.$key.atac_metrics.csv" - } - - - , - "atac_metrics_json": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_metrics_json.json`, example: `ATAC_Metrics.json`. ATAC Metrics JSON", - "help_text": "Type: `file`, default: `$id.$key.atac_metrics_json.json`, example: `ATAC_Metrics.json`. ATAC Metrics JSON. Overall metrics from the ATAC-Seq analysis in JSON format." - , - "default":"$id.$key.atac_metrics_json.json" - } - - - , - "atac_fragments": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_fragments.gz`, example: `ATAC_Fragments.bed.gz`. ATAC Fragments", - "help_text": "Type: `file`, default: `$id.$key.atac_fragments.gz`, example: `ATAC_Fragments.bed.gz`. ATAC Fragments. Chromosomal location, cell index, and read support for each fragment detected" - , - "default":"$id.$key.atac_fragments.gz" - } - - - , - "atac_fragments_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_fragments_index.tbi`, example: `ATAC_Fragments.bed.gz.tbi`. Index of ATAC Fragments", - "help_text": "Type: `file`, default: `$id.$key.atac_fragments_index.tbi`, example: `ATAC_Fragments.bed.gz.tbi`. Index of ATAC Fragments." - , - "default":"$id.$key.atac_fragments_index.tbi" - } - - - , - "atac_transposase_sites": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_transposase_sites.gz`, example: `ATAC_Transposase_Sites.bed.gz`. ATAC Transposase Sites", - "help_text": "Type: `file`, default: `$id.$key.atac_transposase_sites.gz`, example: `ATAC_Transposase_Sites.bed.gz`. ATAC Transposase Sites. Chromosomal location, cell index, and read support for each transposase site detected" - , - "default":"$id.$key.atac_transposase_sites.gz" - } - - - , - "atac_transposase_sites_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_transposase_sites_index.tbi`, example: `ATAC_Transposase_Sites.bed.gz.tbi`. Index of ATAC Transposase Sites", - "help_text": "Type: `file`, default: `$id.$key.atac_transposase_sites_index.tbi`, example: `ATAC_Transposase_Sites.bed.gz.tbi`. Index of ATAC Transposase Sites." - , - "default":"$id.$key.atac_transposase_sites_index.tbi" - } - - - , - "atac_peaks": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_peaks.gz`, example: `ATAC_Peaks.bed.gz`. ATAC Peaks", - "help_text": "Type: `file`, default: `$id.$key.atac_peaks.gz`, example: `ATAC_Peaks.bed.gz`. ATAC Peaks. Peak regions of transposase activity" - , - "default":"$id.$key.atac_peaks.gz" - } - - - , - "atac_peaks_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_peaks_index.tbi`, example: `ATAC_Peaks.bed.gz.tbi`. Index of ATAC Peaks", - "help_text": "Type: `file`, default: `$id.$key.atac_peaks_index.tbi`, example: `ATAC_Peaks.bed.gz.tbi`. Index of ATAC Peaks." - , - "default":"$id.$key.atac_peaks_index.tbi" - } - - - , - "atac_peak_annotation": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_peak_annotation.gz`, example: `peak_annotation.tsv.gz`. ATAC Peak Annotation", - "help_text": "Type: `file`, default: `$id.$key.atac_peak_annotation.gz`, example: `peak_annotation.tsv.gz`. ATAC Peak Annotation. Estimated annotation of peak-to-gene connections" - , - "default":"$id.$key.atac_peak_annotation.gz" - } - - - , - "atac_cell_by_peak": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_cell_by_peak.zip`, example: `ATAC_Cell_by_Peak_MEX.zip`. ATAC Cell by Peak", - "help_text": "Type: `file`, default: `$id.$key.atac_cell_by_peak.zip`, example: `ATAC_Cell_by_Peak_MEX.zip`. ATAC Cell by Peak. Peak regions of transposase activity per cell" - , - "default":"$id.$key.atac_cell_by_peak.zip" - } - - - , - "atac_cell_by_peak_unfiltered": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_cell_by_peak_unfiltered.zip`, example: `ATAC_Cell_by_Peak_Unfiltered_MEX.zip`. ATAC Cell by Peak Unfiltered", - "help_text": "Type: `file`, default: `$id.$key.atac_cell_by_peak_unfiltered.zip`, example: `ATAC_Cell_by_Peak_Unfiltered_MEX.zip`. ATAC Cell by Peak Unfiltered. Unfiltered file containing all cell labels with \u003e=1 transposase sites in peaks." - , - "default":"$id.$key.atac_cell_by_peak_unfiltered.zip" - } - - - , - "atac_bam": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_bam.bam`, example: `ATAC.bam`. ATAC BAM", - "help_text": "Type: `file`, default: `$id.$key.atac_bam.bam`, example: `ATAC.bam`. ATAC BAM. Alignment file for R1 and R2 with associated I2 annotations for ATAC-Seq. Only output if the BAM generation flag is set to true." - , - "default":"$id.$key.atac_bam.bam" - } - - - , - "atac_bam_index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.atac_bam_index.bai`, example: `ATAC.bam.bai`. Index of ATAC BAM", - "help_text": "Type: `file`, default: `$id.$key.atac_bam_index.bai`, example: `ATAC.bam.bai`. Index of ATAC BAM." - , - "default":"$id.$key.atac_bam_index.bai" - } - - -} -}, - - - "abseq cell calling outputs" : { - "title": "AbSeq Cell Calling outputs", - "type": "object", - "description": "Outputs when Cell Calling Abseq is selected", - "properties": { - - - "protein_aggregates_experimental": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.protein_aggregates_experimental.csv`, example: `Protein_Aggregates_Experimental.csv`. Protein Aggregates Experimental", - "help_text": "Type: `file`, default: `$id.$key.protein_aggregates_experimental.csv`, example: `Protein_Aggregates_Experimental.csv`. Protein Aggregates Experimental" - , - "default":"$id.$key.protein_aggregates_experimental.csv" - } - - -} -}, - - - "putative cell calling settings" : { - "title": "Putative Cell Calling Settings", - "type": "object", - "description": "No description", - "properties": { - - - "cell_calling_data": { - "type": - "string", - "description": "Type: `string`, example: `mRNA`, choices: ``mRNA`, `AbSeq`, `ATAC`, `mRNA_and_ATAC``. Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC\n\nFor putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above", - "help_text": "Type: `string`, example: `mRNA`, choices: ``mRNA`, `AbSeq`, `ATAC`, `mRNA_and_ATAC``. Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC\n\nFor putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above.\n\nFor putative cell calling using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file above.\n\nThe default data for putative cell calling, will be determined the following way:\n\n- If mRNA Reads and ATAC Reads exist: mRNA_and_ATAC\n- If only ATAC Reads exist: ATAC\n- Otherwise: mRNA\n", - "enum": ["mRNA", "AbSeq", "ATAC", "mRNA_and_ATAC"] - - - } - - - , - "cell_calling_bioproduct_algorithm": { - "type": - "string", - "description": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling", - "help_text": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling.\n", - "enum": ["Basic", "Refined"] - - - } - - - , - "cell_calling_atac_algorithm": { - "type": - "string", - "description": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling", - "help_text": "Type: `string`, example: `Basic`, choices: ``Basic`, `Refined``. Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling.\n", - "enum": ["Basic", "Refined"] - - - } - - - , - "exact_cell_count": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. Set a specific number (\u003e=1) of cells as putative, based on those with the highest error-corrected read count\n", - "help_text": "Type: `integer`, example: `10000`. Set a specific number (\u003e=1) of cells as putative, based on those with the highest error-corrected read count\n" - - } - - - , - "expected_cell_count": { - "type": - "integer", - "description": "Type: `integer`, example: `20000`. Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected", - "help_text": "Type: `integer`, example: `20000`. Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected. Usually this can be the number of cells loaded into the Rhapsody cartridge. If there are multiple inflection points on the second derivative cumulative curve, this will ensure the one selected is near the expected. \n" - - } - - -} -}, - - - "intronic reads settings" : { - "title": "Intronic Reads Settings", - "type": "object", - "description": "No description", - "properties": { - - - "exclude_intronic_reads": { - "type": - "boolean", - "description": "Type: `boolean`, example: `false`. By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts", - "help_text": "Type: `boolean`, example: `false`. By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts. When the flag is set to true, intronic reads will be excluded.\nThe value can be true or false.\n" - - } - - -} -}, - - - "multiplex settings" : { - "title": "Multiplex Settings", - "type": "object", - "description": "No description", - "properties": { - - - "sample_tags_version": { - "type": - "string", - "description": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `flex`, `nuclei_includes_mrna`, `nuclei_atac_only``. Specify the version of the Sample Tags used in the run:\n\n* If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only\n* If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the \"nuclei_includes_mrna\" option", - "help_text": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `flex`, `nuclei_includes_mrna`, `nuclei_atac_only``. Specify the version of the Sample Tags used in the run:\n\n* If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only\n* If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the \"nuclei_includes_mrna\" option.\n* If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)), choose the \"nuclei_atac_only\" option.\n", - "enum": ["human", "mouse", "flex", "nuclei_includes_mrna", "nuclei_atac_only"] - - - } - - - , - "tag_names": { - "type": - "string", - "description": "Type: List of `string`, example: `4-mySample;9-myOtherSample;6-alsoThisSample`, multiple_sep: `\";\"`. Specify the tag number followed by \u0027-\u0027 and the desired sample name to appear in Sample_Tag_Metrics", - "help_text": "Type: List of `string`, example: `4-mySample;9-myOtherSample;6-alsoThisSample`, multiple_sep: `\";\"`. Specify the tag number followed by \u0027-\u0027 and the desired sample name to appear in Sample_Tag_Metrics.csv\nDo not use the special characters: \u0026, (), [], {}, \u003c\u003e, ?, |\n" - - } - - -} -}, - - - "vdj arguments" : { - "title": "VDJ arguments", - "type": "object", - "description": "No description", - "properties": { - - - "vdj_version": { - "type": - "string", - "description": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `humanBCR`, `humanTCR`, `mouseBCR`, `mouseTCR``. If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR\n", - "help_text": "Type: `string`, example: `human`, choices: ``human`, `mouse`, `humanBCR`, `humanTCR`, `mouseBCR`, `mouseTCR``. If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR\n", - "enum": ["human", "mouse", "humanBCR", "humanTCR", "mouseBCR", "mouseTCR"] - - - } - - -} -}, - - - "atac options" : { - "title": "ATAC options", - "type": "object", - "description": "No description", - "properties": { - - - "predefined_atac_peaks": { - "type": - "string", - "description": "Type: `file`, example: `predefined_peaks.bed`. An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix", - "help_text": "Type: `file`, example: `predefined_peaks.bed`. An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix." - - } - - -} -}, - - - "additional options" : { - "title": "Additional options", - "type": "object", - "description": "No description", - "properties": { - - - "run_name": { - "type": - "string", - "description": "Type: `string`, default: `sample`. Specify a run name to use as the output file base name", - "help_text": "Type: `string`, default: `sample`. Specify a run name to use as the output file base name. Use only letters, numbers, or hyphens. Do not use special characters or spaces.\n" - , - "default":"sample" - } - - - , - "generate_bam": { - "type": - "boolean", - "description": "Type: `boolean`, default: `false`. Specify whether to create the BAM file output\n", - "help_text": "Type: `boolean`, default: `false`. Specify whether to create the BAM file output\n" - , - "default":false - } - - - , - "long_reads": { - "type": - "boolean", - "description": "Type: `boolean`. Use STARlong (default: undefined - i", - "help_text": "Type: `boolean`. Use STARlong (default: undefined - i.e. autodetects based on read lengths) - Specify if the STARlong aligner should be used instead of STAR. Set to true if the reads are longer than 650bp.\n" - - } - - -} -}, - - - "advanced options" : { - "title": "Advanced options", - "type": "object", - "description": "NOTE: Only change these if you are really sure about what you are doing\n", - "properties": { - - - "custom_star_params": { - "type": - "string", - "description": "Type: `string`, example: `--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000`. Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline", - "help_text": "Type: `string`, example: `--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000`. Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline.\nFor reference this is the default that is used:\n\n Short Reads: `--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin 25 --limitOutSJcollapsed 2000000`\n Long Reads: Same as Short Reads + `--seedPerReadNmax 10000`\n\nThis applies to fastqs provided in the Reads user input \nDo NOT set any non-mapping related params like `--genomeDir`, `--outSAMtype`, `--outSAMunmapped`, `--readFilesIn`, `--runThreadN`, etc.\nWe use STAR version 2.7.10b\n" - - } - - - , - "custom_bwa_mem2_params": { - "type": - "string", - "description": "Type: `string`, example: `-k 16 -w 200 -r`. Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline\nThe pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used\nThis applies to fastqs provided in the Reads_ATAC user input \nDo NOT set any non-mapping related params like `-C`, `-t`, etc", - "help_text": "Type: `string`, example: `-k 16 -w 200 -r`. Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline\nThe pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used\nThis applies to fastqs provided in the Reads_ATAC user input \nDo NOT set any non-mapping related params like `-C`, `-t`, etc.\nWe use bwa-mem2 version 2.2.1\n" - - } - - -} -}, - - - "cwl-runner arguments" : { - "title": "CWL-runner arguments", - "type": "object", - "description": "No description", - "properties": { - - - "parallel": { - "type": - "boolean", - "description": "Type: `boolean`, default: `true`. Run jobs in parallel", - "help_text": "Type: `boolean`, default: `true`. Run jobs in parallel." - , - "default":true - } - - - , - "timestamps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add timestamps to the errors, warnings, and notifications", - "help_text": "Type: `boolean_true`, default: `false`. Add timestamps to the errors, warnings, and notifications." - , - "default":false - } - - -} -}, - - - "undocumented arguments" : { - "title": "Undocumented arguments", - "type": "object", - "description": "No description", - "properties": { - - - "abseq_umi": { - "type": - "integer", - "description": "Type: `integer`. ", - "help_text": "Type: `integer`. " - - } - - - , - "target_analysis": { - "type": - "boolean", - "description": "Type: `boolean`. ", - "help_text": "Type: `boolean`. " - - } - - - , - "vdj_jgene_evalue": { - "type": - "number", - "description": "Type: `double`. e-value threshold for J gene", - "help_text": "Type: `double`. e-value threshold for J gene. The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001\n" - - } - - - , - "vdj_vgene_evalue": { - "type": - "number", - "description": "Type: `double`. e-value threshold for V gene", - "help_text": "Type: `double`. e-value threshold for V gene. The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001\n" - - } - - - , - "write_filtered_reads": { - "type": - "boolean", - "description": "Type: `boolean`. ", - "help_text": "Type: `boolean`. " - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bd_rhapsody_sequence_analysis", + "description": "BD Rhapsody Sequence Analysis CWL pipeline v2.2.\n\nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody™ assay kits, including: Whole Transcriptome\nmRNA (WTA), Targeted mRNA, AbSeq Antibody-Oligonucleotides (ABC), Single-Cell Multiplexing (SMK),\nTCR/BCR (VDJ), and ATAC-Seq.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "reads": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Reads (optional) - Path to your FASTQ.GZ formatted read files from libraries that may include:\n\n- WTA mRNA\n- Targeted mRNA\n- AbSeq\n- Sample Multiplexing\n- VDJ\n\nYou may specify as many R1/R2 read pairs as you want.\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"WTALibrary_S1_L001_R1_001.fastq.gz\";\"WTALibrary_S1_L001_R2_001.fastq.gz\"]`. " + }, + "reads_atac": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries.\nYou may specify as many R1/R2/I2 files as you want.\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"ATACLibrary_S2_L001_R1_001.fastq.gz\";\"ATACLibrary_S2_L001_R2_001.fastq.gz\";\"ATACLibrary_S2_L001_I2_001.fastq.gz\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "Outputs for all pipeline runs", + "properties": { + "output_dir": { + "type": "string", + "format": "path", + "description": "The unprocessed output directory containing all the outputs from the pipeline.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_dir\"`, direction: `output`, example: `\"output_dir\"`. ", + "default": "$id.$key.output_dir" + }, + "output_seurat": { + "type": "string", + "format": "path", + "description": "Single-cell analysis tool inputs", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_seurat.rds\"`, direction: `output`, example: `\"output_seurat.rds\"`. ", + "default": "$id.$key.output_seurat.rds" + }, + "output_mudata": { + "type": "string", + "format": "path", + "description": "Single-cell analysis tool inputs", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_mudata.h5mu\"`, direction: `output`, example: `\"output_mudata.h5mu\"`. ", + "default": "$id.$key.output_mudata.h5mu" + }, + "metrics_summary": { + "type": "string", + "format": "path", + "description": "Metrics Summary", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.metrics_summary.csv\"`, direction: `output`, example: `\"metrics_summary.csv\"`. ", + "default": "$id.$key.metrics_summary.csv" + }, + "pipeline_report": { + "type": "string", + "format": "path", + "description": "Pipeline Report", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.pipeline_report.html\"`, direction: `output`, example: `\"pipeline_report.html\"`. ", + "default": "$id.$key.pipeline_report.html" + }, + "rsec_mols_per_cell": { + "type": "string", + "format": "path", + "description": "Molecules per bioproduct per cell bassed on RSEC", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.rsec_mols_per_cell.zip\"`, direction: `output`, example: `\"RSEC_MolsPerCell_MEX.zip\"`. ", + "default": "$id.$key.rsec_mols_per_cell.zip" + }, + "dbec_mols_per_cell": { + "type": "string", + "format": "path", + "description": "Molecules per bioproduct per cell bassed on DBEC", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.dbec_mols_per_cell.zip\"`, direction: `output`, example: `\"DBEC_MolsPerCell_MEX.zip\"`. ", + "default": "$id.$key.dbec_mols_per_cell.zip" + }, + "rsec_mols_per_cell_unfiltered": { + "type": "string", + "format": "path", + "description": "Unfiltered tables containing all cell labels with ≥10 reads.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.rsec_mols_per_cell_unfiltered.zip\"`, direction: `output`, example: `\"RSEC_MolsPerCell_Unfiltered_MEX.zip\"`. ", + "default": "$id.$key.rsec_mols_per_cell_unfiltered.zip" + }, + "bam": { + "type": "string", + "format": "path", + "description": "Alignment file of R2 with associated R1 annotations for Bioproduct.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam.bam\"`, direction: `output`, example: `\"BioProduct.bam\"`. ", + "default": "$id.$key.bam.bam" + }, + "bam_index": { + "type": "string", + "format": "path", + "description": "Index file for the alignment file.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam_index.bai\"`, direction: `output`, example: `\"BioProduct.bam.bai\"`. ", + "default": "$id.$key.bam_index.bai" + }, + "bioproduct_stats": { + "type": "string", + "format": "path", + "description": "Bioproduct Stats", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bioproduct_stats.csv\"`, direction: `output`, example: `\"Bioproduct_Stats.csv\"`. ", + "default": "$id.$key.bioproduct_stats.csv" + }, + "dimred_tsne": { + "type": "string", + "format": "path", + "description": "t-SNE dimensionality reduction coordinates per cell index", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.dimred_tsne.csv\"`, direction: `output`, example: `\"tSNE_coordinates.csv\"`. ", + "default": "$id.$key.dimred_tsne.csv" + }, + "dimred_umap": { + "type": "string", + "format": "path", + "description": "UMAP dimensionality reduction coordinates per cell index", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.dimred_umap.csv\"`, direction: `output`, example: `\"UMAP_coordinates.csv\"`. ", + "default": "$id.$key.dimred_umap.csv" + }, + "immune_cell_classification": { + "type": "string", + "format": "path", + "description": "Immune Cell Classification", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.immune_cell_classification.csv\"`, direction: `output`, example: `\"Immune_Cell_Classification.csv\"`. ", + "default": "$id.$key.immune_cell_classification.csv" + } + } }, - - { - "$ref": "#/definitions/references" + "references": { + "title": "References", + "type": "object", + "description": "Assay type will be inferred from the provided reference(s).\nDo not provide both reference_archive and targeted_reference at the same time.\n\nValid reference input combinations:\n - reference_archive: WTA only\n - reference_archive & abseq_reference: WTA + AbSeq\n - reference_archive & supplemental_reference: WTA + extra transgenes\n - reference_archive & abseq_reference & supplemental_reference: WTA + AbSeq + extra transgenes\n - reference_archive: WTA + ATAC or ATAC only\n - reference_archive & supplemental_reference: WTA + ATAC + extra transgenes\n - targeted_reference: Targeted only\n - targeted_reference & abseq_reference: Targeted + AbSeq\n - abseq_reference: AbSeq only\n\nThe reference_archive can be generated with the bd_rhapsody_make_reference component.\nAlternatively, BD also provides standard references which can be downloaded from these locations:\n\n - Human: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Human_WTA_2023-02.tar.gz\n - Mouse: https://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-WTA/Pipeline-version2.x_WTA_references/RhapRef_Mouse_WTA_2023-02.tar.gz\n", + "properties": { + "reference_archive": { + "type": "string", + "format": "path", + "description": "Path to Rhapsody WTA Reference in the tar.gz format.\n\nStructure of the reference archive:\n\n- `BD_Rhapsody_Reference_Files/`: top level folder\n - `star_index/`: sub-folder containing STAR index, that is files created with `STAR --runMode genomeGenerate`\n - GTF for gene-transcript-annotation e.g", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"RhapRef_Human_WTA_2023-02.tar.gz\"`. " + }, + "targeted_reference": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Path to the targeted reference file in FASTA format.\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"BD_Rhapsody_Immune_Response_Panel_Hs.fasta\"]`. " + }, + "abseq_reference": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Path to the AbSeq reference file in FASTA format", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"AbSeq_reference.fasta\"]`. " + }, + "supplemental_reference": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Path to the supplemental reference file in FASTA format", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"supplemental_reference.fasta\"]`. " + } + } }, - - { - "$ref": "#/definitions/multiplex outputs" + "multiplex outputs": { + "title": "Multiplex outputs", + "type": "object", + "description": "Outputs when multiplex option is selected", + "properties": { + "sample_tag_metrics": { + "type": "string", + "format": "path", + "description": "Sample Tag Metrics", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sample_tag_metrics.csv\"`, direction: `output`, example: `\"Sample_Tag_Metrics.csv\"`. ", + "default": "$id.$key.sample_tag_metrics.csv" + }, + "sample_tag_calls": { + "type": "string", + "format": "path", + "description": "Sample Tag Calls", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sample_tag_calls.csv\"`, direction: `output`, example: `\"Sample_Tag_Calls.csv\"`. ", + "default": "$id.$key.sample_tag_calls.csv" + }, + "sample_tag_counts": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Sample Tag Counts", + "help_text": "Type: `file`, multiple: `True`, default: `\"$id.$key.sample_tag_counts_*.zip\"`, direction: `output`, example: `[\"Sample_Tag1.zip\"]`. ", + "default": "$id.$key.sample_tag_counts_*.zip" + }, + "sample_tag_counts_unassigned": { + "type": "string", + "format": "path", + "description": "Sample Tag Counts Unassigned", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sample_tag_counts_unassigned.zip\"`, direction: `output`, example: `\"Multiplet_and_Undetermined.zip\"`. ", + "default": "$id.$key.sample_tag_counts_unassigned.zip" + } + } }, - - { - "$ref": "#/definitions/vdj outputs" + "vdj outputs": { + "title": "VDJ Outputs", + "type": "object", + "description": "Outputs when VDJ option selected", + "properties": { + "vdj_metrics": { + "type": "string", + "format": "path", + "description": "VDJ Metrics", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.vdj_metrics.csv\"`, direction: `output`, example: `\"VDJ_Metrics.csv\"`. ", + "default": "$id.$key.vdj_metrics.csv" + }, + "vdj_per_cell": { + "type": "string", + "format": "path", + "description": "VDJ Per Cell", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.vdj_per_cell.csv\"`, direction: `output`, example: `\"VDJ_perCell.csv\"`. ", + "default": "$id.$key.vdj_per_cell.csv" + }, + "vdj_per_cell_uncorrected": { + "type": "string", + "format": "path", + "description": "VDJ Per Cell Uncorrected", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.vdj_per_cell_uncorrected.csv\"`, direction: `output`, example: `\"VDJ_perCell_uncorrected.csv\"`. ", + "default": "$id.$key.vdj_per_cell_uncorrected.csv" + }, + "vdj_dominant_contigs": { + "type": "string", + "format": "path", + "description": "VDJ Dominant Contigs", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.vdj_dominant_contigs.csv\"`, direction: `output`, example: `\"VDJ_Dominant_Contigs_AIRR.csv\"`. ", + "default": "$id.$key.vdj_dominant_contigs.csv" + }, + "vdj_unfiltered_contigs": { + "type": "string", + "format": "path", + "description": "VDJ Unfiltered Contigs", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.vdj_unfiltered_contigs.csv\"`, direction: `output`, example: `\"VDJ_Unfiltered_Contigs_AIRR.csv\"`. ", + "default": "$id.$key.vdj_unfiltered_contigs.csv" + } + } }, - - { - "$ref": "#/definitions/atac-seq outputs" + "atac-seq outputs": { + "title": "ATAC-Seq outputs", + "type": "object", + "description": "Outputs when ATAC-Seq option selected", + "properties": { + "atac_metrics": { + "type": "string", + "format": "path", + "description": "ATAC Metrics", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_metrics.csv\"`, direction: `output`, example: `\"ATAC_Metrics.csv\"`. ", + "default": "$id.$key.atac_metrics.csv" + }, + "atac_metrics_json": { + "type": "string", + "format": "path", + "description": "ATAC Metrics JSON", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_metrics_json.json\"`, direction: `output`, example: `\"ATAC_Metrics.json\"`. ", + "default": "$id.$key.atac_metrics_json.json" + }, + "atac_fragments": { + "type": "string", + "format": "path", + "description": "ATAC Fragments", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_fragments.gz\"`, direction: `output`, example: `\"ATAC_Fragments.bed.gz\"`. ", + "default": "$id.$key.atac_fragments.gz" + }, + "atac_fragments_index": { + "type": "string", + "format": "path", + "description": "Index of ATAC Fragments.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_fragments_index.tbi\"`, direction: `output`, example: `\"ATAC_Fragments.bed.gz.tbi\"`. ", + "default": "$id.$key.atac_fragments_index.tbi" + }, + "atac_transposase_sites": { + "type": "string", + "format": "path", + "description": "ATAC Transposase Sites", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_transposase_sites.gz\"`, direction: `output`, example: `\"ATAC_Transposase_Sites.bed.gz\"`. ", + "default": "$id.$key.atac_transposase_sites.gz" + }, + "atac_transposase_sites_index": { + "type": "string", + "format": "path", + "description": "Index of ATAC Transposase Sites.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_transposase_sites_index.tbi\"`, direction: `output`, example: `\"ATAC_Transposase_Sites.bed.gz.tbi\"`. ", + "default": "$id.$key.atac_transposase_sites_index.tbi" + }, + "atac_peaks": { + "type": "string", + "format": "path", + "description": "ATAC Peaks", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_peaks.gz\"`, direction: `output`, example: `\"ATAC_Peaks.bed.gz\"`. ", + "default": "$id.$key.atac_peaks.gz" + }, + "atac_peaks_index": { + "type": "string", + "format": "path", + "description": "Index of ATAC Peaks.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_peaks_index.tbi\"`, direction: `output`, example: `\"ATAC_Peaks.bed.gz.tbi\"`. ", + "default": "$id.$key.atac_peaks_index.tbi" + }, + "atac_peak_annotation": { + "type": "string", + "format": "path", + "description": "ATAC Peak Annotation", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_peak_annotation.gz\"`, direction: `output`, example: `\"peak_annotation.tsv.gz\"`. ", + "default": "$id.$key.atac_peak_annotation.gz" + }, + "atac_cell_by_peak": { + "type": "string", + "format": "path", + "description": "ATAC Cell by Peak", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_cell_by_peak.zip\"`, direction: `output`, example: `\"ATAC_Cell_by_Peak_MEX.zip\"`. ", + "default": "$id.$key.atac_cell_by_peak.zip" + }, + "atac_cell_by_peak_unfiltered": { + "type": "string", + "format": "path", + "description": "ATAC Cell by Peak Unfiltered", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_cell_by_peak_unfiltered.zip\"`, direction: `output`, example: `\"ATAC_Cell_by_Peak_Unfiltered_MEX.zip\"`. ", + "default": "$id.$key.atac_cell_by_peak_unfiltered.zip" + }, + "atac_bam": { + "type": "string", + "format": "path", + "description": "ATAC BAM", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_bam.bam\"`, direction: `output`, example: `\"ATAC.bam\"`. ", + "default": "$id.$key.atac_bam.bam" + }, + "atac_bam_index": { + "type": "string", + "format": "path", + "description": "Index of ATAC BAM.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.atac_bam_index.bai\"`, direction: `output`, example: `\"ATAC.bam.bai\"`. ", + "default": "$id.$key.atac_bam_index.bai" + } + } }, - - { - "$ref": "#/definitions/abseq cell calling outputs" + "abseq cell calling outputs": { + "title": "AbSeq Cell Calling outputs", + "type": "object", + "description": "Outputs when Cell Calling Abseq is selected", + "properties": { + "protein_aggregates_experimental": { + "type": "string", + "format": "path", + "description": "Protein Aggregates Experimental", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.protein_aggregates_experimental.csv\"`, direction: `output`, example: `\"Protein_Aggregates_Experimental.csv\"`. ", + "default": "$id.$key.protein_aggregates_experimental.csv" + } + } }, - - { - "$ref": "#/definitions/putative cell calling settings" + "putative cell calling settings": { + "title": "Putative Cell Calling Settings", + "type": "object", + "description": "No description", + "properties": { + "cell_calling_data": { + "type": "string", + "description": "Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC\n\nFor putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above.\n\nFor putative cell calling using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file above.\n\nThe default data for putative cell calling, will be determined the following way:\n\n- If mRNA Reads and ATAC Reads exist: mRNA_and_ATAC\n- If only ATAC Reads exist: ATAC\n- Otherwise: mRNA\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"mRNA\"`, choices: ``mRNA`, `AbSeq`, `ATAC`, `mRNA_and_ATAC``. ", + "enum": [ + "mRNA", + "AbSeq", + "ATAC", + "mRNA_and_ATAC" + ] + }, + "cell_calling_bioproduct_algorithm": { + "type": "string", + "description": "Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"Basic\"`, choices: ``Basic`, `Refined``. ", + "enum": [ + "Basic", + "Refined" + ] + }, + "cell_calling_atac_algorithm": { + "type": "string", + "description": "Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined\n\nBy default, the Basic algorithm will be used for putative cell calling.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"Basic\"`, choices: ``Basic`, `Refined``. ", + "enum": [ + "Basic", + "Refined" + ] + }, + "exact_cell_count": { + "type": "integer", + "description": "Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count\n", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "expected_cell_count": { + "type": "integer", + "description": "Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected", + "help_text": "Type: `integer`, multiple: `False`, example: `20000`. " + } + } }, - - { - "$ref": "#/definitions/intronic reads settings" + "intronic reads settings": { + "title": "Intronic Reads Settings", + "type": "object", + "description": "No description", + "properties": { + "exclude_intronic_reads": { + "type": "boolean", + "description": "By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts", + "help_text": "Type: `boolean`, multiple: `False`, example: `false`. " + } + } }, - - { - "$ref": "#/definitions/multiplex settings" + "multiplex settings": { + "title": "Multiplex Settings", + "type": "object", + "description": "No description", + "properties": { + "sample_tags_version": { + "type": "string", + "description": "Specify the version of the Sample Tags used in the run:\n\n* If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only\n* If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the \"nuclei_includes_mrna\" option.\n* If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)), choose the \"nuclei_atac_only\" option.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"human\"`, choices: ``human`, `mouse`, `flex`, `nuclei_includes_mrna`, `nuclei_atac_only``. ", + "enum": [ + "human", + "mouse", + "flex", + "nuclei_includes_mrna", + "nuclei_atac_only" + ] + }, + "tag_names": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Specify the tag number followed by '-' and the desired sample name to appear in Sample_Tag_Metrics.csv\nDo not use the special characters: &, (), [], {}, <>, ?, |\n", + "help_text": "Type: `string`, multiple: `True`, example: `[\"4-mySample\";\"9-myOtherSample\";\"6-alsoThisSample\"]`. " + } + } }, - - { - "$ref": "#/definitions/vdj arguments" + "vdj arguments": { + "title": "VDJ arguments", + "type": "object", + "description": "No description", + "properties": { + "vdj_version": { + "type": "string", + "description": "If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"human\"`, choices: ``human`, `mouse`, `humanBCR`, `humanTCR`, `mouseBCR`, `mouseTCR``. ", + "enum": [ + "human", + "mouse", + "humanBCR", + "humanTCR", + "mouseBCR", + "mouseTCR" + ] + } + } }, - - { - "$ref": "#/definitions/atac options" + "atac options": { + "title": "ATAC options", + "type": "object", + "description": "No description", + "properties": { + "predefined_atac_peaks": { + "type": "string", + "format": "path", + "description": "An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"predefined_peaks.bed\"`. " + } + } }, - - { - "$ref": "#/definitions/additional options" + "additional options": { + "title": "Additional options", + "type": "object", + "description": "No description", + "properties": { + "run_name": { + "type": "string", + "description": "Specify a run name to use as the output file base name", + "help_text": "Type: `string`, multiple: `False`, default: `\"sample\"`. ", + "default": "sample" + }, + "generate_bam": { + "type": "boolean", + "description": "Specify whether to create the BAM file output\n", + "help_text": "Type: `boolean`, multiple: `False`, default: `false`. ", + "default": false + }, + "long_reads": { + "type": "boolean", + "description": "Use STARlong (default: undefined - i.e", + "help_text": "Type: `boolean`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/advanced options" + "advanced options": { + "title": "Advanced options", + "type": "object", + "description": "NOTE: Only change these if you are really sure about what you are doing\n", + "properties": { + "custom_star_params": { + "type": "string", + "description": "Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline.\nFor reference this is the default that is used:\n\n Short Reads: `--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin 25 --limitOutSJcollapsed 2000000`\n Long Reads: Same as Short Reads + `--seedPerReadNmax 10000`\n\nThis applies to fastqs provided in the Reads user input \nDo NOT set any non-mapping related params like `--genomeDir`, `--outSAMtype`, `--outSAMunmapped`, `--readFilesIn`, `--runThreadN`, etc.\nWe use STAR version 2.7.10b\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"--alignIntronMax 6000 --outFilterScoreMinOverLread 0.1 --limitOutSJcollapsed 2000000\"`. " + }, + "custom_bwa_mem2_params": { + "type": "string", + "description": "Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline\nThe pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used\nThis applies to fastqs provided in the Reads_ATAC user input \nDo NOT set any non-mapping related params like `-C`, `-t`, etc.\nWe use bwa-mem2 version 2.2.1\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"-k 16 -w 200 -r\"`. " + } + } }, - - { - "$ref": "#/definitions/cwl-runner arguments" + "cwl-runner arguments": { + "title": "CWL-runner arguments", + "type": "object", + "description": "No description", + "properties": { + "parallel": { + "type": "boolean", + "description": "Run jobs in parallel.", + "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ", + "default": true + }, + "timestamps": { + "type": "boolean", + "description": "Add timestamps to the errors, warnings, and notifications.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/undocumented arguments" + "undocumented arguments": { + "title": "Undocumented arguments", + "type": "object", + "description": "No description", + "properties": { + "abseq_umi": { + "type": "integer", + "description": "", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "target_analysis": { + "type": "boolean", + "description": "", + "help_text": "Type: `boolean`, multiple: `False`. " + }, + "vdj_jgene_evalue": { + "type": "number", + "description": "e-value threshold for J gene", + "help_text": "Type: `double`, multiple: `False`. " + }, + "vdj_vgene_evalue": { + "type": "number", + "description": "e-value threshold for V gene", + "help_text": "Type: `double`, multiple: `False`. " + }, + "write_filtered_reads": { + "type": "boolean", + "description": "", + "help_text": "Type: `boolean`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/references" + }, + { + "$ref": "#/$defs/multiplex outputs" + }, + { + "$ref": "#/$defs/vdj outputs" + }, + { + "$ref": "#/$defs/atac-seq outputs" + }, + { + "$ref": "#/$defs/abseq cell calling outputs" + }, + { + "$ref": "#/$defs/putative cell calling settings" + }, + { + "$ref": "#/$defs/intronic reads settings" + }, + { + "$ref": "#/$defs/multiplex settings" + }, + { + "$ref": "#/$defs/vdj arguments" + }, + { + "$ref": "#/$defs/atac options" + }, + { + "$ref": "#/$defs/additional options" + }, + { + "$ref": "#/$defs/advanced options" + }, + { + "$ref": "#/$defs/cwl-runner arguments" + }, + { + "$ref": "#/$defs/undocumented arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml index f7503c34..cb466d52 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -238,9 +234,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtobed" executable: "target/nextflow/bedtools/bedtools_bamtobed/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -265,6 +261,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtobed/main.nf b/target/nextflow/bedtools/bedtools_bamtobed/main.nf index 9f50c45d..21b0192e 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtobed/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3331,9 +3324,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtobed", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3349,6 +3342,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json index 4d266fca..be1e839f 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json @@ -1,206 +1,121 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_bamtobed", -"description": "Converts BAM alignments to BED6 or BEDPE format.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input BAM file", - "help_text": "Type: `file`, required. Input BAM file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output BED file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output BED file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "bedpe": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write BEDPE format", - "help_text": "Type: `boolean_true`, default: `false`. Write BEDPE format. Requires BAM to be grouped or sorted by query.\n" - , - "default":false - } - - - , - "mate1": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\"", - "help_text": "Type: `boolean_true`, default: `false`. When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\".\n" - , - "default":false - } - - - , - "bed12": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write \"blocked\" BED format (aka \"BED12\")", - "help_text": "Type: `boolean_true`, default: `false`. Write \"blocked\" BED format (aka \"BED12\"). Forces -split.\nSee http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1\n" - , - "default":false - } - - - , - "split": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report \"split\" BAM alignments as separate BED entries", - "help_text": "Type: `boolean_true`, default: `false`. Report \"split\" BAM alignments as separate BED entries.\nSplits only on N CIGAR operations.\n" - , - "default":false - } - - - , - "splitD": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Split alignments based on N and D CIGAR operators", - "help_text": "Type: `boolean_true`, default: `false`. Split alignments based on N and D CIGAR operators.\nForces -split.\n" - , - "default":false - } - - - , - "edit_distance": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use BAM edit distance (NM tag) for BED score", - "help_text": "Type: `boolean_true`, default: `false`. Use BAM edit distance (NM tag) for BED score.\n- Default for BED is to use mapping quality.\n- Default for BEDPE is to use the minimum of\n the two mapping qualities for the pair.\n- When -ed is used with -bedpe, the total edit\n distance from the two mates is reported.\n" - , - "default":false - } - - - , - "tag": { - "type": - "string", - "description": "Type: `string`, example: `SM`. Use other NUMERIC BAM alignment tag for BED score", - "help_text": "Type: `string`, example: `SM`. Use other NUMERIC BAM alignment tag for BED score.\nDefault for BED is to use mapping quality. Disallowed with BEDPE output.\n" - - } - - - , - "color": { - "type": - "string", - "description": "Type: `string`, example: `250,250,250`. An R,G,B string for the color used with BED12 format", - "help_text": "Type: `string`, example: `250,250,250`. An R,G,B string for the color used with BED12 format.\nDefault is (255,0,0).\n" - - } - - - , - "cigar": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add the CIGAR string to the BED entry as a 7th column", - "help_text": "Type: `boolean_true`, default: `false`. Add the CIGAR string to the BED entry as a 7th column.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_bamtobed", + "description": "Converts BAM alignments to BED6 or BEDPE format.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BAM file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output BED file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "bedpe": { + "type": "boolean", + "description": "Write BEDPE format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mate1": { + "type": "boolean", + "description": "When writing BEDPE (-bedpe) format, always report mate one as the first BEDPE \"block\".\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed12": { + "type": "boolean", + "description": "Write \"blocked\" BED format (aka \"BED12\")", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "split": { + "type": "boolean", + "description": "Report \"split\" BAM alignments as separate BED entries.\nSplits only on N CIGAR operations.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "splitD": { + "type": "boolean", + "description": "Split alignments based on N and D CIGAR operators.\nForces -split.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "edit_distance": { + "type": "boolean", + "description": "Use BAM edit distance (NM tag) for BED score.\n- Default for BED is to use mapping quality.\n- Default for BEDPE is to use the minimum of\n the two mapping qualities for the pair.\n- When -ed is used with -bedpe, the total edit\n distance from the two mates is reported.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "tag": { + "type": "string", + "description": "Use other NUMERIC BAM alignment tag for BED score.\nDefault for BED is to use mapping quality", + "help_text": "Type: `string`, multiple: `False`, example: `\"SM\"`. " + }, + "color": { + "type": "string", + "description": "An R,G,B string for the color used with BED12 format.\nDefault is (255,0,0).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"250,250,250\"`. " + }, + "cigar": { + "type": "boolean", + "description": "Add the CIGAR string to the BED entry as a 7th column.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index aeae5e58..05b88ec6 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -190,9 +186,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -217,6 +213,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 1af68d30..0c7e3ec7 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3280,9 +3273,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3298,6 +3291,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json index b88a7bd4..387aa40e 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json @@ -1,131 +1,82 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_bamtofastq", -"description": "Conversion tool for extracting FASTQ records from sequence alignments in BAM format.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input BAM file to be converted to FASTQ", - "help_text": "Type: `file`, required. Input BAM file to be converted to FASTQ." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "fastq": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.fastq`. Output FASTQ file", - "help_text": "Type: `file`, required, default: `$id.$key.fastq`. Output FASTQ file." - , - "default":"$id.$key.fastq" - } - - - , - "fastq2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fastq2`. FASTQ for second end", - "help_text": "Type: `file`, default: `$id.$key.fastq2`. FASTQ for second end. Used if BAM contains paired-end data.\nBAM should be sorted by query name is creating paired FASTQ.\n" - , - "default":"$id.$key.fastq2" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "tags": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Create FASTQ based on the mate info in the BAM R2 and Q2 tags", - "help_text": "Type: `boolean_true`, default: `false`. Create FASTQ based on the mate info in the BAM R2 and Q2 tags.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_bamtofastq", + "description": "Conversion tool for extracting FASTQ records from sequence alignments in BAM format.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BAM file to be converted to FASTQ.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "fastq": { + "type": "string", + "format": "path", + "description": "Output FASTQ file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.fastq\"`, direction: `output`. ", + "default": "$id.$key.fastq" + }, + "fastq2": { + "type": "string", + "format": "path", + "description": "FASTQ for second end", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq2\"`, direction: `output`. ", + "default": "$id.$key.fastq2" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "tags": { + "type": "boolean", + "description": "Create FASTQ based on the mate info in the BAM R2 and Q2 tags.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index 5bf0ca86..58ec6ce9 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -179,9 +175,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -206,6 +202,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index 8f216d13..5412b3a7 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3265,9 +3258,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3283,6 +3276,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json index efbe0c2a..60bf232e 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json @@ -1,120 +1,75 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_bed12tobed6", -"description": "Converts BED features in BED12 (a.k.a. \u201cblocked\u201d BED features such as genes) to discrete BED6 features.\nFor example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input BED12 file", - "help_text": "Type: `file`, required. Input BED12 file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Output BED6 file to be written", - "help_text": "Type: `file`, default: `$id.$key.output`. Output BED6 file to be written." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "n_score": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force the score to be the (1-based) block number from the BED12", - "help_text": "Type: `boolean_true`, default: `false`. Force the score to be the (1-based) block number from the BED12.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_bed12tobed6", + "description": "Converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features.\nFor example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BED12 file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output BED6 file to be written.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "n_score": { + "type": "boolean", + "description": "Force the score to be the (1-based) block number from the BED12.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index f4f50d8c..aeca146c 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -217,9 +213,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -244,6 +240,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index 0ec21d15..1154a1c0 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3313,9 +3306,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3331,6 +3324,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json index a3ee084c..35971e37 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json @@ -1,152 +1,94 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_bedtobam", -"description": "Converts feature records (bed/gff/vcf) to BAM format.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file (bed/gff/vcf)", - "help_text": "Type: `file`, required. Input file (bed/gff/vcf)." - - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`, required. Input genome file", - "help_text": "Type: `file`, required. Input genome file.\nNOTE: This is not a fasta file. This is a two-column tab-delimited file\nwhere the first column is the chromosome name and the second their sizes.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Output BAM file to be written", - "help_text": "Type: `file`, default: `$id.$key.output`. Output BAM file to be written." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "map_quality": { - "type": - "integer", - "description": "Type: `integer`, default: `255`. Set the mappinq quality for the BAM records", - "help_text": "Type: `integer`, default: `255`. Set the mappinq quality for the BAM records.\n" - , - "default":255 - } - - - , - "bed12": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. The BED file is in BED12 format", - "help_text": "Type: `boolean_true`, default: `false`. The BED file is in BED12 format. The BAM CIGAR\nstring will reflect BED \"blocks\".\n" - , - "default":false - } - - - , - "uncompress_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output", - "help_text": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output. Default writes compressed BAM.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_bedtobam", + "description": "Converts feature records (bed/gff/vcf) to BAM format.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file (bed/gff/vcf).", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "genome": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input genome file.\nNOTE: This is not a fasta file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output BAM file to be written.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "map_quality": { + "type": "integer", + "description": "Set the mappinq quality for the BAM records.\n", + "help_text": "Type: `integer`, multiple: `False`, default: `255`. ", + "default": 255 + }, + "bed12": { + "type": "boolean", + "description": "The BED file is in BED12 format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "uncompress_bam": { + "type": "boolean", + "description": "Write uncompressed BAM output", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index b7a14b5f..12ffaeb9 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -340,9 +336,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -367,6 +363,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index 9bd242fc..e5ab11a2 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3437,9 +3430,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_genomecov", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3455,6 +3448,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json index 292d2515..b90f7940 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json @@ -1,303 +1,179 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_genomecov", -"description": "Compute the coverage of a feature file among a genome.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, example: `input.bed`. The input file (BED/GFF/VCF) to be used", - "help_text": "Type: `file`, example: `input.bed`. The input file (BED/GFF/VCF) to be used.\n" - - } - - - , - "input_bam": { - "type": - "string", - "description": "Type: `file`. The input file is in BAM format", - "help_text": "Type: `file`. The input file is in BAM format.\nNote: BAM _must_ be sorted by positions.\n\u0027--genome\u0027 option is ignored if you use \u0027--input_bam\u0027 option!\n" - - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`, example: `genome.txt`. The genome file to be used", - "help_text": "Type: `file`, example: `genome.txt`. The genome file to be used.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file", - "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n" - , - "default":"$id.$key.output.bed" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "depth": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates)", - "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n" - , - "default":false - } - - - , - "depth_zero": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates)", - "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" - , - "default":false - } - - - , - "bed_graph": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format", - "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" - , - "default":false - } - - - , - "bed_graph_zero_coverage": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg)", - "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0 \ncoverage by applying: \"grep -w 0$\" to the output.\n" - , - "default":false - } - - - , - "split": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals", - "help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" - , - "default":false - } - - - , - "ignore_deletion": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage", - "help_text": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage.\n" - , - "default":false - } - - - , - "strand": { - "type": - "string", - "description": "Type: `string`, choices: ``+`, `-``. Calculate coverage of intervals from a specific strand", - "help_text": "Type: `string`, choices: ``+`, `-``. Calculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6). \n", - "enum": ["+", "-"] - - - } - - - , - "pair_end_coverage": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments", - "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments.\nWorks for BAM files only\n" - , - "default":false - } - - - , - "fragment_size": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n", - "help_text": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n" - , - "default":false - } - - - , - "du": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n", - "help_text": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n" - , - "default":false - } - - - , - "five_prime": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval)", - "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval).\n" - , - "default":false - } - - - , - "three_prime": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval)", - "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval).\n" - , - "default":false - } - - - , - "max": { - "type": - "integer", - "description": "Type: `integer`. Combine all positions with a depth \u003e= max into\na single bin in the histogram", - "help_text": "Type: `integer`. Combine all positions with a depth \u003e= max into\na single bin in the histogram. Irrelevant\nfor -d and -bedGraph\n- (INTEGER)\n" - - } - - - , - "scale": { - "type": - "number", - "description": "Type: `double`. Scale the coverage by a constant factor", - "help_text": "Type: `double`. Scale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n" - - } - - - , - "trackline": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output", - "help_text": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" - , - "default":false - } - - - , - "trackopts": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Writes additional track line definition parameters in the first line", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Writes additional track line definition parameters in the first line.\n- Example:\n -trackopts \u0027name=\"My Track\" visibility=2 color=255,30,30\u0027\n Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_genomecov", + "description": "Compute the coverage of a feature file among a genome.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "description": "The input file (BED/GFF/VCF) to be used.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"input.bed\"`. " + }, + "input_bam": { + "type": "string", + "format": "path", + "description": "The input file is in BAM format.\nNote: BAM _must_ be sorted by positions.\n'--genome' option is ignored if you use '--input_bam' option!\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "genome": { + "type": "string", + "format": "path", + "description": "The genome file to be used.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.txt\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output BED file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"output.bed\"`. ", + "default": "$id.$key.output.bed" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "depth": { + "type": "boolean", + "description": "Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "depth_zero": { + "type": "boolean", + "description": "Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed_graph": { + "type": "boolean", + "description": "Report depth in BedGraph format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed_graph_zero_coverage": { + "type": "boolean", + "description": "Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "split": { + "type": "boolean", + "description": "Treat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ignore_deletion": { + "type": "boolean", + "description": "Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "strand": { + "type": "string", + "description": "Calculate coverage of intervals from a specific strand.\nWith BED files, requires at least 6 columns (strand is column 6)", + "help_text": "Type: `string`, multiple: `False`, choices: ``+`, `-``. ", + "enum": [ + "+", + "-" + ] + }, + "pair_end_coverage": { + "type": "boolean", + "description": "Calculate coverage of pair-end fragments.\nWorks for BAM files only\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fragment_size": { + "type": "boolean", + "description": "Force to use provided fragment size instead of read length\nWorks for BAM files only\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "du": { + "type": "boolean", + "description": "Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "five_prime": { + "type": "boolean", + "description": "Calculate coverage of 5\" positions (instead of entire interval).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "three_prime": { + "type": "boolean", + "description": "Calculate coverage of 3\" positions (instead of entire interval).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "max": { + "type": "integer", + "description": "Combine all positions with a depth >= max into\na single bin in the histogram", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "scale": { + "type": "number", + "description": "Scale the coverage by a constant factor.\nEach coverage value is multiplied by this factor before being reported.\nUseful for normalizing coverage by, e.g., reads per million (RPM).\n- Default is 1.0; i.e., unscaled.\n- (FLOAT)\n", + "help_text": "Type: `double`, multiple: `False`. " + }, + "trackline": { + "type": "boolean", + "description": "Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "trackopts": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Writes additional track line definition parameters in the first line.\n- Example:\n -trackopts 'name=\"My Track\" visibility=2 color=255,30,30'\n Note the use of single-quotes if you have spaces in your parameters.\n- (TEXT)\n", + "help_text": "Type: `string`, multiple: `True`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index f0157ee9..933833d1 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -262,6 +262,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 9da1f169..edb01201 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3316,9 +3316,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3334,6 +3334,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json index ea17c4e6..a4ceb0a9 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json @@ -1,207 +1,122 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_getfasta", -"description": "Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.", -"type": "object", -"definitions": { - - - - "input arguments" : { - "title": "Input arguments", - "type": "object", - "description": "No description", - "properties": { - - - "input_fasta": { - "type": - "string", - "description": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file", - "help_text": "Type: `file`. FASTA file containing sequences for each interval specified in the input BED file.\nThe headers in the input FASTA file must exactly match the chromosome column in the BED file.\n" - - } - - - , - "input_bed": { - "type": - "string", - "description": "Type: `file`. BED file containing intervals to extract from the FASTA file", - "help_text": "Type: `file`. BED file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n" - - } - - - , - "rna": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA", - "help_text": "Type: `boolean_true`, default: `false`. The FASTA is RNA not DNA. Reverse complementation handled accordingly.\n" - , - "default":false - } - - -} -}, - - - "run arguments" : { - "title": "Run arguments", - "type": "object", - "description": "No description", - "properties": { - - - "strandedness": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force strandedness", - "help_text": "Type: `boolean_true`, default: `false`. Force strandedness. If the feature occupies the antisense strand, the output sequence will\nbe reverse complemented. By default strandedness is not taken into account.\n" - , - "default":false - } - - -} -}, - - - "output arguments" : { - "title": "Output arguments", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n" - , - "default":"$id.$key.output" - } - - - , - "tab": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format", - "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited format instead of in FASTA format.\n" - , - "default":false - } - - - , - "bed_out": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format", - "help_text": "Type: `boolean_true`, default: `false`. Report extract sequences in a tab-delimited BED format instead of in FASTA format.\n" - , - "default":false - } - - - , - "name": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature", - "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature.\n" - , - "default":false - } - - - , - "name_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature", - "help_text": "Type: `boolean_true`, default: `false`. Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature.\n" - , - "default":false - } - - - , - "split": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED", - "help_text": "Type: `boolean_true`, default: `false`. When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED.\n" - , - "default":false - } - - - , - "full_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use full fasta header", - "help_text": "Type: `boolean_true`, default: `false`. Use full fasta header. By default, only the word before the first space or tab is used.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_getfasta", + "description": "Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.", + "type": "object", + "$defs": { + "input arguments": { + "title": "Input arguments", + "type": "object", + "description": "No description", + "properties": { + "input_fasta": { + "type": "string", + "format": "path", + "description": "FASTA file containing sequences for each interval specified in the input BED file.\nThe headers in the input FASTA file must exactly match the chromosome column in the BED file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "input_bed": { + "type": "string", + "format": "path", + "description": "BED file containing intervals to extract from the FASTA file.\nBED files containing a single region require a newline character\nat the end of the line, otherwise a blank output file is produced.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "rna": { + "type": "boolean", + "description": "The FASTA is RNA not DNA", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/run arguments" + "run arguments": { + "title": "Run arguments", + "type": "object", + "description": "No description", + "properties": { + "strandedness": { + "type": "boolean", + "description": "Force strandedness", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/output arguments" + "output arguments": { + "title": "Output arguments", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file where the output from the 'bedtools getfasta' commend will\nbe written to.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + }, + "tab": { + "type": "boolean", + "description": "Report extract sequences in a tab-delimited format instead of in FASTA format.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed_out": { + "type": "boolean", + "description": "Report extract sequences in a tab-delimited BED format instead of in FASTA format.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "name": { + "type": "boolean", + "description": "Set the FASTA header for each extracted sequence to be the \"name\" and coordinate columns from the BED feature.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "name_only": { + "type": "boolean", + "description": "Set the FASTA header for each extracted sequence to be the \"name\" columns from the BED feature.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "split": { + "type": "boolean", + "description": "When --input is in BED12 format, create a separate fasta entry for each block in a BED12 record,\nblocks being described in the 11th and 12th column of the BED.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "full_header": { + "type": "boolean", + "description": "Use full fasta header", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input arguments" + }, + { + "$ref": "#/$defs/run arguments" + }, + { + "$ref": "#/$defs/output arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index 2b57a758..2e8b859c 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -276,9 +272,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -303,6 +299,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index 8b1debc3..63ac984a 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3360,9 +3353,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3378,6 +3371,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json b/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json index c1896c1e..11161aee 100644 --- a/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json @@ -1,216 +1,126 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_groupby", -"description": "Summarizes a dataset column based upon common column groupings. \nAkin to the SQL \"group by\" command.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `input_a.bed`. The input BED file to be used", - "help_text": "Type: `file`, required, example: `input_a.bed`. The input BED file to be used.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output groupby BED file", - "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output groupby BED file. \n" - , - "default":"$id.$key.output.bed" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "groupby": { - "type": - "string", - "description": "Type: `string`, required. Specify the columns (1-based) for the grouping", - "help_text": "Type: `string`, required. Specify the columns (1-based) for the grouping.\nThe columns must be comma separated.\n- Default: 1,2,3 \n" - - } - - - , - "column": { - "type": - "integer", - "description": "Type: `integer`, required. Specify the column (1-based) that should be summarized", - "help_text": "Type: `integer`, required. Specify the column (1-based) that should be summarized.\n" - - } - - - , - "operation": { - "type": - "string", - "description": "Type: `string`. Specify the operation that should be applied to opCol", - "help_text": "Type: `string`. Specify the operation that should be applied to opCol.\nValid operations:\n sum, count, count_distinct, min, max,\n mean, median, mode, antimode,\n stdev, sstdev (sample standard dev.),\n collapse (i.e., print a comma separated list (duplicates allowed)), \n distinct (i.e., print a comma separated list (NO duplicates allowed)), \n distinct_sort_num (as distinct, but sorted numerically, ascending), \n distinct_sort_num_desc (as distinct, but sorted numerically, descending), \n concat (i.e., merge values into a single, non-delimited string), \n freqdesc (i.e., print desc. list of values:freq)\n freqasc (i.e., print asc. list of values:freq)\n first (i.e., print first value)\n last (i.e., print last value)\n\nDefault value: sum \n\nIf there is only column, but multiple operations, all operations will be\napplied on that column. Likewise, if there is only one operation, but\nmultiple columns, that operation will be applied to all columns.\nOtherwise, the number of columns must match the the number of operations,\nand will be applied in respective order.\nE.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,\nthe mean of column 4, and the count of column 6.\nThe order of output columns will match the ordering given in the command.\n" - - } - - - , - "full": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print all columns from input file", - "help_text": "Type: `boolean_true`, default: `false`. Print all columns from input file. The first line in the group is used.\nDefault: print only grouped columns.\n" - , - "default":false - } - - - , - "inheader": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input file has a header line - the first line will be ignored", - "help_text": "Type: `boolean_true`, default: `false`. Input file has a header line - the first line will be ignored.\n" - , - "default":false - } - - - , - "outheader": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print header line in the output, detailing the column names", - "help_text": "Type: `boolean_true`, default: `false`. Print header line in the output, detailing the column names. \nIf the input file has headers (-inheader), the output file\nwill use the input\u0027s column names.\nIf the input file has no headers, the output file\nwill use \"col_1\", \"col_2\", etc. as the column names.\n" - , - "default":false - } - - - , - "header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. same as \u0027-inheader -outheader\u0027", - "help_text": "Type: `boolean_true`, default: `false`. same as \u0027-inheader -outheader\u0027." - , - "default":false - } - - - , - "ignorecase": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Group values regardless of upper/lower case", - "help_text": "Type: `boolean_true`, default: `false`. Group values regardless of upper/lower case.\n" - , - "default":false - } - - - , - "precision": { - "type": - "integer", - "description": "Type: `integer`, default: `5`. Sets the decimal precision for output", - "help_text": "Type: `integer`, default: `5`. Sets the decimal precision for output. \n" - , - "default":5 - } - - - , - "delimiter": { - "type": - "string", - "description": "Type: `string`, default: `,`, example: `|`. Specify a custom delimiter for the collapse operations", - "help_text": "Type: `string`, default: `,`, example: `|`. Specify a custom delimiter for the collapse operations.\n" - , - "default":"," - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_groupby", + "description": "Summarizes a dataset column based upon common column groupings. \nAkin to the SQL \"group by\" command.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "The input BED file to be used.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input_a.bed\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output groupby BED file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"output.bed\"`. ", + "default": "$id.$key.output.bed" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "groupby": { + "type": "string", + "description": "Specify the columns (1-based) for the grouping.\nThe columns must be comma separated.\n- Default: 1,2,3 \n", + "help_text": "Type: `string`, multiple: `False`, required. " + }, + "column": { + "type": "integer", + "description": "Specify the column (1-based) that should be summarized.\n", + "help_text": "Type: `integer`, multiple: `False`, required. " + }, + "operation": { + "type": "string", + "description": "Specify the operation that should be applied to opCol.\nValid operations:\n sum, count, count_distinct, min, max,\n mean, median, mode, antimode,\n stdev, sstdev (sample standard dev.),\n collapse (i.e., print a comma separated list (duplicates allowed)), \n distinct (i.e., print a comma separated list (NO duplicates allowed)), \n distinct_sort_num (as distinct, but sorted numerically, ascending), \n distinct_sort_num_desc (as distinct, but sorted numerically, descending), \n concat (i.e., merge values into a single, non-delimited string), \n freqdesc (i.e., print desc", + "help_text": "Type: `string`, multiple: `False`. " + }, + "full": { + "type": "boolean", + "description": "Print all columns from input file", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "inheader": { + "type": "boolean", + "description": "Input file has a header line - the first line will be ignored.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "outheader": { + "type": "boolean", + "description": "Print header line in the output, detailing the column names", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "header": { + "type": "boolean", + "description": "same as '-inheader -outheader'.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ignorecase": { + "type": "boolean", + "description": "Group values regardless of upper/lower case.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "precision": { + "type": "integer", + "description": "Sets the decimal precision for output", + "help_text": "Type: `integer`, multiple: `False`, default: `5`. ", + "default": 5 + }, + "delimiter": { + "type": "string", + "description": "Specify a custom delimiter for the collapse operations.\n", + "help_text": "Type: `string`, multiple: `False`, default: `\",\"`, example: `\"|\"`. ", + "default": "," + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index e7dc5721..3615af14 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -413,9 +409,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -440,6 +436,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 89a3842c..788577cb 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3512,9 +3505,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3530,6 +3523,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json b/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json index 5345ee1a..21d400a5 100644 --- a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json @@ -1,400 +1,231 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_intersect", -"description": "bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input_a": { - "type": - "string", - "description": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file", - "help_text": "Type: `file`, required, example: `input_a.bed`. The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n" - - } - - - , - "input_b": { - "type": - "string", - "description": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\";\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)", - "help_text": "Type: List of `file`, required, example: `input_b.bed`, multiple_sep: `\";\"`. The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file", - "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n" - , - "default":"$id.$key.output.bed" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "write_a": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap", - "help_text": "Type: `boolean_true`, default: `false`. Write the original A entry for each overlap." - , - "default":false - } - - - , - "write_b": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap", - "help_text": "Type: `boolean_true`, default: `false`. Write the original B entry for each overlap. \nUseful for knowing _what_ A overlaps. Restricted by -f and -r.\n" - , - "default":false - } - - - , - "left_outer_join": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\"", - "help_text": "Type: `boolean_true`, default: `false`. Perform a \"left outer join\". That is, for each feature in A report each overlap with B. \nIf no overlaps are found, report a NULL feature for B.\n" - , - "default":false - } - - - , - "write_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features", - "help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n Only A features with overlap are reported.\n" - , - "default":false - } - - - , - "write_overlap_plus": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features", - "help_text": "Type: `boolean_true`, default: `false`. Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r. \n However, A features w/o overlap are also reported with a NULL B feature and overlap = 0.\n" - , - "default":false - } - - - , - "report_A_if_no_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found", - "help_text": "Type: `boolean_true`, default: `false`. Write the original A entry _if_ no overlap is found. \n- In other words, just report the fact \u003e=1 hit was found.\n- Overlaps restricted by -f and -r. \n" - , - "default":false - } - - - , - "number_of_overlaps_A": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B", - "help_text": "Type: `boolean_true`, default: `false`. For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n" - , - "default":false - } - - - , - "report_no_overlaps_A": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B", - "help_text": "Type: `boolean_true`, default: `false`. Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n" - , - "default":false - } - - - , - "uncompressed_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output", - "help_text": "Type: `boolean_true`, default: `false`. Write uncompressed BAM output. Default writes compressed BAM." - , - "default":false - } - - - , - "same_strand": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Require same strandedness", - "help_text": "Type: `boolean_true`, default: `false`. Require same strandedness. That is, only report hits in B.\nthat overlap A on the _same_ strand.\n- By default, overlaps are reported without respect to strand.\n" - , - "default":false - } - - - , - "opposite_strand": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Require different strandedness", - "help_text": "Type: `boolean_true`, default: `false`. Require different strandedness. That is, only report hits in B\nthat overlap A on the _opposite_ strand.\n- By default, overlaps are reported without respect to strand.\n" - , - "default":false - } - - - , - "min_overlap_A": { - "type": - "number", - "description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A", - "help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" - - } - - - , - "min_overlap_B": { - "type": - "number", - "description": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B", - "help_text": "Type: `double`, example: `0.5`. Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g. 0.50)\n" - - } - - - , - "reciprocal_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B", - "help_text": "Type: `boolean_true`, default: `false`. Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90% of A and A _also_ overlaps 90% of B.\n" - , - "default":false - } - - - , - "either_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B", - "help_text": "Type: `boolean_true`, default: `false`. Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would have to be satisfied.\n" - , - "default":false - } - - - , - "split": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals", - "help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals." - , - "default":false - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files", - "help_text": "Type: `file`, example: `genome.txt`. Provide a genome file to enforce consistent chromosome \nsort order across input files. Only applies when used \nwith -sorted option.\n" - - } - - - , - "nonamecheck": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e", - "help_text": "Type: `boolean_true`, default: `false`. For sorted data, don\u0027t throw an error if the file \nhas different naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\").\n" - , - "default":false - } - - - , - "sorted": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input", - "help_text": "Type: `boolean_true`, default: `false`. Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n" - , - "default":false - } - - - , - "names": { - "type": - "string", - "description": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record", - "help_text": "Type: `string`. When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record.\n" - - } - - - , - "filenames": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record", - "help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, show each complete filename instead of a fileId when also printing the DB record." - , - "default":false - } - - - , - "sortout": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record", - "help_text": "Type: `boolean_true`, default: `false`. When using multiple databases, sort the output DB hits for each record." - , - "default":false - } - - - , - "bed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED", - "help_text": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED." - , - "default":false - } - - - , - "header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results", - "help_text": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results." - , - "default":false - } - - - , - "no_buffer_output": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable buffered output", - "help_text": "Type: `boolean_true`, default: `false`. Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files \nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n" - , - "default":false - } - - - , - "io_buffer_size": { - "type": - "integer", - "description": "Type: `integer`. Specify amount of memory to use for input buffer", - "help_text": "Type: `integer`. Specify amount of memory to use for input buffer.\nTakes an integer argument. Optional suffixes K/M/G supported.\nNote: currently has no effect with compressed files. \n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_intersect", + "description": "bedtools intersect allows one to screen for overlaps between two sets of genomic features. \nMoreover, it allows one to have fine control as to how the intersections are reported. \nbedtools intersect works with both BED/GFF/VCF and BAM files as input.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input_a": { + "type": "string", + "format": "path", + "exists": true, + "description": "The input file (BED/GFF/VCF/BAM) to be used as the -a file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input_a.bed\"`. " + }, + "input_b": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s).\n", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input_b.bed\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output BED file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"output.bed\"`. ", + "default": "$id.$key.output.bed" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "write_a": { + "type": "boolean", + "description": "Write the original A entry for each overlap.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "write_b": { + "type": "boolean", + "description": "Write the original B entry for each overlap", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "left_outer_join": { + "type": "boolean", + "description": "Perform a \"left outer join\"", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "write_overlap": { + "type": "boolean", + "description": "Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "write_overlap_plus": { + "type": "boolean", + "description": "Write the original A and B entries plus the number of base pairs of overlap between the two features.\n- Overlaps restricted by -f and -r", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "report_A_if_no_overlap": { + "type": "boolean", + "description": "Write the original A entry _if_ no overlap is found", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "number_of_overlaps_A": { + "type": "boolean", + "description": "For each entry in A, report the number of overlaps with B.\n- Reports 0 for A entries that have no overlap with B.\n- Overlaps restricted by -f and -r.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "report_no_overlaps_A": { + "type": "boolean", + "description": "Only report those entries in A that have _no overlaps_ with B.\n- Similar to \"grep -v\" (an homage).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "uncompressed_bam": { + "type": "boolean", + "description": "Write uncompressed BAM output", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "same_strand": { + "type": "boolean", + "description": "Require same strandedness", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "opposite_strand": { + "type": "boolean", + "description": "Require different strandedness", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_overlap_A": { + "type": "number", + "description": "Minimum overlap required as a fraction of A.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g", + "help_text": "Type: `double`, multiple: `False`, example: `0.5`. " + }, + "min_overlap_B": { + "type": "number", + "description": "Minimum overlap required as a fraction of B.\n- Default is 1E-9 (i.e., 1bp).\n- FLOAT (e.g", + "help_text": "Type: `double`, multiple: `False`, example: `0.5`. " + }, + "reciprocal_overlap": { + "type": "boolean", + "description": "Require that the fraction overlap be reciprocal for A AND B.\n- In other words, if -f is 0.90 and -r is used, this requires\nthat B overlap 90% of A and A _also_ overlaps 90% of B.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "either_overlap": { + "type": "boolean", + "description": "Require that the minimum fraction be satisfied for A OR B.\n- In other words, if -e is used with -f 0.90 and -F 0.10 this requires\nthat either 90% of A is covered OR 10% of B is covered.\nWithout -e, both fractions would have to be satisfied.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "split": { + "type": "boolean", + "description": "Treat \"split\" BAM or BED12 entries as distinct BED intervals.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "genome": { + "type": "string", + "format": "path", + "description": "Provide a genome file to enforce consistent chromosome \nsort order across input files", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.txt\"`. " + }, + "nonamecheck": { + "type": "boolean", + "description": "For sorted data, don't throw an error if the file \nhas different naming conventions for the same chromosome \n(e.g., \"chr1\" vs \"chr01\").\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sorted": { + "type": "boolean", + "description": "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "names": { + "type": "string", + "description": "When using multiple databases, provide an alias \nfor each that will appear instead of a fileId when \nalso printing the DB record.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "filenames": { + "type": "boolean", + "description": "When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sortout": { + "type": "boolean", + "description": "When using multiple databases, sort the output DB hits for each record.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed": { + "type": "boolean", + "description": "If using BAM input, write output as BED.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "header": { + "type": "boolean", + "description": "Print the header from the A file prior to results.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_buffer_output": { + "type": "boolean", + "description": "Disable buffered output", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "io_buffer_size": { + "type": "integer", + "description": "Specify amount of memory to use for input buffer.\nTakes an integer argument", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index 80f3c3f9..c13385ad 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -213,9 +209,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -240,6 +236,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index 15942d0b..28082dae 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3303,9 +3296,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3321,6 +3314,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json index 61084c87..3ed2302c 100644 --- a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json @@ -1,142 +1,87 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_links", -"description": "Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. \nThis is useful for cases when one wants to manually inspect through a large set of annotations or features.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file (bed/gff/vcf)", - "help_text": "Type: `file`, required. Input file (bed/gff/vcf)." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Output HTML file to be written", - "help_text": "Type: `file`, default: `$id.$key.output`. Output HTML file to be written." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "By default, the links created will point to human (hg18) UCSC browser.\nIf you have a local mirror, you can override this behavior by supplying\nthe -base, -org, and -db options.\n\nFor example, if the URL of your local mirror for mouse MM9 is called: \nhttp://mymirror.myuniversity.edu, then you would use the following:\n--base_url http://mymirror.myuniversity.edu\n--organism mouse\n--database mm9\n", - "properties": { - - - "base_url": { - "type": - "string", - "description": "Type: `string`, default: `http://genome.ucsc.edu`. The \u201cbasename\u201d for the UCSC browser", - "help_text": "Type: `string`, default: `http://genome.ucsc.edu`. The \u201cbasename\u201d for the UCSC browser.\n" - , - "default":"http://genome.ucsc.edu" - } - - - , - "organism": { - "type": - "string", - "description": "Type: `string`, default: `human`. The organism (e", - "help_text": "Type: `string`, default: `human`. The organism (e.g. mouse, human). \n" - , - "default":"human" - } - - - , - "database": { - "type": - "string", - "description": "Type: `string`, default: `hg18`. The genome build", - "help_text": "Type: `string`, default: `hg18`. The genome build. \n" - , - "default":"hg18" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_links", + "description": "Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a file. \nThis is useful for cases when one wants to manually inspect through a large set of annotations or features.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file (bed/gff/vcf).", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output HTML file to be written.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "By default, the links created will point to human (hg18) UCSC browser.\nIf you have a local mirror, you can override this behavior by supplying\nthe -base, -org, and -db options.\n\nFor example, if the URL of your local mirror for mouse MM9 is called: \nhttp://mymirror.myuniversity.edu, then you would use the following:\n--base_url http://mymirror.myuniversity.edu\n--organism mouse\n--database mm9\n", + "properties": { + "base_url": { + "type": "string", + "description": "The “basename” for the UCSC browser.\n", + "help_text": "Type: `string`, multiple: `False`, default: `\"http://genome.ucsc.edu\"`. ", + "default": "http://genome.ucsc.edu" + }, + "organism": { + "type": "string", + "description": "The organism (e.g", + "help_text": "Type: `string`, multiple: `False`, default: `\"human\"`. ", + "default": "human" + }, + "database": { + "type": "string", + "description": "The genome build", + "help_text": "Type: `string`, multiple: `False`, default: `\"hg18\"`. ", + "default": "hg18" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 23505e4a..0891cff5 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -282,9 +278,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -309,6 +305,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index b7cc9d6e..e39c7adc 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3364,9 +3357,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3382,6 +3375,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json index 1abef291..030c293a 100644 --- a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json @@ -1,216 +1,128 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_merge", -"description": "Merges overlapping BED/GFF/VCF entries into a single interval.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file (BED/GFF/VCF) to be merged", - "help_text": "Type: `file`, required. Input file (BED/GFF/VCF) to be merged." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output merged file BED to be written", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output merged file BED to be written." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "strand": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force strandedness", - "help_text": "Type: `boolean_true`, default: `false`. Force strandedness. That is, only merge features\nthat are on the same strand.\n- By default, merging is done without respect to strand.\n" - , - "default":false - } - - - , - "specific_strand": { - "type": - "string", - "description": "Type: `string`, choices: ``+`, `-``. Force merge for one specific strand only", - "help_text": "Type: `string`, choices: ``+`, `-``. Force merge for one specific strand only.\nFollow with + or - to force merge from only\nthe forward or reverse strand, respectively.\n- By default, merging is done without respect to strand.\n", - "enum": ["+", "-"] - - - } - - - , - "distance": { - "type": - "integer", - "description": "Type: `integer`. Maximum distance between features allowed for features\nto be merged", - "help_text": "Type: `integer`. Maximum distance between features allowed for features\nto be merged.\n- Def. 0. That is, overlapping \u0026 book-ended features are merged.\n- (INTEGER)\n- Note: negative values enforce the number of b.p. required for overlap.\n" - - } - - - , - "columns": { - "type": - "integer", - "description": "Type: `integer`. Specify columns from the B file to map onto intervals in A", - "help_text": "Type: `integer`. Specify columns from the B file to map onto intervals in A.\nDefault: 5.\nMultiple columns can be specified in a comma-delimited list.\n" - - } - - - , - "operation": { - "type": - "string", - "description": "Type: `string`. Specify the operation that should be applied to -c", - "help_text": "Type: `string`. Specify the operation that should be applied to -c.\nValid operations:\n sum, min, max, absmin, absmax,\n mean, median, mode, antimode\n stdev, sstdev\n collapse (i.e., print a delimited list (duplicates allowed)), \n distinct (i.e., print a delimited list (NO duplicates allowed)), \n distinct_sort_num (as distinct, sorted numerically, ascending),\n distinct_sort_num_desc (as distinct, sorted numerically, desscending),\n distinct_only (delimited list of only unique values),\n count\n count_distinct (i.e., a count of the unique values in the column), \n first (i.e., just the first value in the column), \n last (i.e., just the last value in the column), \nDefault: sum\nMultiple operations can be specified in a comma-delimited list.\n\nIf there is only column, but multiple operations, all operations will be\napplied on that column. Likewise, if there is only one operation, but\nmultiple columns, that operation will be applied to all columns.\nOtherwise, the number of columns must match the the number of operations,\nand will be applied in respective order.\nE.g., \"-c 5,4,6 -o sum,mean,count\" will give the sum of column 5,\nthe mean of column 4, and the count of column 6.\nThe order of output columns will match the ordering given in the command.\n" - - } - - - , - "delimiter": { - "type": - "string", - "description": "Type: `string`, default: `,`, example: `|`. Specify a custom delimiter for the collapse operations", - "help_text": "Type: `string`, default: `,`, example: `|`. Specify a custom delimiter for the collapse operations.\n" - , - "default":"," - } - - - , - "precision": { - "type": - "integer", - "description": "Type: `integer`. Sets the decimal precision for output (Default: 5)", - "help_text": "Type: `integer`. Sets the decimal precision for output (Default: 5).\n" - - } - - - , - "bed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED", - "help_text": "Type: `boolean_true`, default: `false`. If using BAM input, write output as BED.\n" - , - "default":false - } - - - , - "header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results", - "help_text": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results.\n" - , - "default":false - } - - - , - "no_buffer": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable buffered output", - "help_text": "Type: `boolean_true`, default: `false`. Disable buffered output. Using this option will cause each line\nof output to be printed as it is generated, rather than saved\nin a buffer. This will make printing large output files \nnoticeably slower, but can be useful in conjunction with\nother software tools and scripts that need to process one\nline of bedtools output at a time.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_merge", + "description": "Merges overlapping BED/GFF/VCF entries into a single interval.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file (BED/GFF/VCF) to be merged.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output merged file BED to be written.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "strand": { + "type": "boolean", + "description": "Force strandedness", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "specific_strand": { + "type": "string", + "description": "Force merge for one specific strand only.\nFollow with + or - to force merge from only\nthe forward or reverse strand, respectively.\n- By default, merging is done without respect to strand.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``+`, `-``. ", + "enum": [ + "+", + "-" + ] + }, + "distance": { + "type": "integer", + "description": "Maximum distance between features allowed for features\nto be merged.\n- Def", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "columns": { + "type": "integer", + "description": "Specify columns from the B file to map onto intervals in A.\nDefault: 5.\nMultiple columns can be specified in a comma-delimited list.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "operation": { + "type": "string", + "description": "Specify the operation that should be applied to -c.\nValid operations:\n sum, min, max, absmin, absmax,\n mean, median, mode, antimode\n stdev, sstdev\n collapse (i.e., print a delimited list (duplicates allowed)), \n distinct (i.e., print a delimited list (NO duplicates allowed)), \n distinct_sort_num (as distinct, sorted numerically, ascending),\n distinct_sort_num_desc (as distinct, sorted numerically, desscending),\n distinct_only (delimited list of only unique values),\n count\n count_distinct (i.e., a count of the unique values in the column), \n first (i.e., just the first value in the column), \n last (i.e., just the last value in the column), \nDefault: sum\nMultiple operations can be specified in a comma-delimited list.\n\nIf there is only column, but multiple operations, all operations will be\napplied on that column", + "help_text": "Type: `string`, multiple: `False`. " + }, + "delimiter": { + "type": "string", + "description": "Specify a custom delimiter for the collapse operations.\n", + "help_text": "Type: `string`, multiple: `False`, default: `\",\"`, example: `\"|\"`. ", + "default": "," + }, + "precision": { + "type": "integer", + "description": "Sets the decimal precision for output (Default: 5).\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "bed": { + "type": "boolean", + "description": "If using BAM input, write output as BED.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "header": { + "type": "boolean", + "description": "Print the header from the A file prior to results.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_buffer": { + "type": "boolean", + "description": "Disable buffered output", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 68f0c095..ecaba3a8 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -225,9 +221,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -252,6 +248,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index 90bf940f..e4cc8b07 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3322,9 +3315,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3340,6 +3333,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json index 06b57afd..6031422c 100644 --- a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json @@ -1,206 +1,123 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "bedtools_sort", -"description": "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file (bed/gff/vcf) to be sorted", - "help_text": "Type: `file`, required. Input file (bed/gff/vcf) to be sorted." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Output sorted file (bed/gff/vcf) to be written", - "help_text": "Type: `file`, default: `$id.$key.output`. Output sorted file (bed/gff/vcf) to be written." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "sizeA": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by feature size in ascending order", - "help_text": "Type: `boolean_true`, default: `false`. Sort by feature size in ascending order." - , - "default":false - } - - - , - "sizeD": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by feature size in descending order", - "help_text": "Type: `boolean_true`, default: `false`. Sort by feature size in descending order." - , - "default":false - } - - - , - "chrThenSizeA": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then feature size (asc)", - "help_text": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then feature size (asc)." - , - "default":false - } - - - , - "chrThenSizeD": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then feature size (desc)", - "help_text": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then feature size (desc)." - , - "default":false - } - - - , - "chrThenScoreA": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then score (asc)", - "help_text": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then score (asc)." - , - "default":false - } - - - , - "chrThenScoreD": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then score (desc)", - "help_text": "Type: `boolean_true`, default: `false`. Sort by chrom (asc), then score (desc)." - , - "default":false - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`. Sort according to the chromosomes declared in \"genome", - "help_text": "Type: `file`. Sort according to the chromosomes declared in \"genome.txt\"" - - } - - - , - "faidx": { - "type": - "string", - "description": "Type: `file`. Sort according to the chromosomes declared in \"names", - "help_text": "Type: `file`. Sort according to the chromosomes declared in \"names.txt\"" - - } - - - , - "header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results", - "help_text": "Type: `boolean_true`, default: `false`. Print the header from the A file prior to results." - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "bedtools_sort", + "description": "Sorts a feature file (bed/gff/vcf) by chromosome and other criteria.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file (bed/gff/vcf) to be sorted.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output sorted file (bed/gff/vcf) to be written.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "sizeA": { + "type": "boolean", + "description": "Sort by feature size in ascending order.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sizeD": { + "type": "boolean", + "description": "Sort by feature size in descending order.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chrThenSizeA": { + "type": "boolean", + "description": "Sort by chrom (asc), then feature size (asc).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chrThenSizeD": { + "type": "boolean", + "description": "Sort by chrom (asc), then feature size (desc).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chrThenScoreA": { + "type": "boolean", + "description": "Sort by chrom (asc), then score (asc).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chrThenScoreD": { + "type": "boolean", + "description": "Sort by chrom (asc), then score (desc).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "genome": { + "type": "string", + "format": "path", + "description": "Sort according to the chromosomes declared in \"genome.txt\"", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "faidx": { + "type": "string", + "format": "path", + "description": "Sort according to the chromosomes declared in \"names.txt\"", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "header": { + "type": "boolean", + "description": "Print the header from the A file prior to results.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 512c911e..0da5c9a3 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -161,9 +161,9 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -188,6 +188,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 6a98501b..bd408f74 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -3241,9 +3241,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3259,6 +3259,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json index 5f010260..ed6193cd 100644 --- a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json @@ -1,95 +1,57 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "busco_download_datasets", -"description": "Downloads available busco datasets", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "download": { - "type": - "string", - "description": "Type: `string`, required, example: `stramenopiles_odb10`. Download dataset", - "help_text": "Type: `string`, required, example: `stramenopiles_odb10`. Download dataset. Possible values are a specific dataset name, \"all\", \"prokaryota\", \"eukaryota\", or \"virus\".\nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "download_path": { - "type": - "string", - "description": "Type: `file`, default: `busco_downloads`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n", - "help_text": "Type: `file`, default: `busco_downloads`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n" - , - "default":"busco_downloads" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "busco_download_datasets", + "description": "Downloads available busco datasets", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "download": { + "type": "string", + "description": "Download dataset", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"stramenopiles_odb10\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "download_path": { + "type": "string", + "format": "path", + "description": "Local filepath for storing BUSCO dataset downloads\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"busco_downloads\"`, direction: `output`, example: `\"busco_downloads\"`. ", + "default": "busco_downloads" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index c4216f60..e1ae52c9 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -148,9 +148,9 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -175,6 +175,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 97c30d3e..0af968f5 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -3227,9 +3227,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3245,6 +3245,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json index 40c4b729..9eaa0f33 100644 --- a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json @@ -1,71 +1,42 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "busco_list_datasets", -"description": "Lists the available busco datasets", -"type": "object", -"definitions": { - - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `busco_dataset_list.txt`, example: `file.txt`. Output file of the available busco datasets\n", - "help_text": "Type: `file`, default: `busco_dataset_list.txt`, example: `file.txt`. Output file of the available busco datasets\n" - , - "default":"busco_dataset_list.txt" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/outputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "busco_list_datasets", + "description": "Lists the available busco datasets", + "type": "object", + "$defs": { + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file of the available busco datasets\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"busco_dataset_list.txt\"`, direction: `output`, example: `\"file.txt\"`. ", + "default": "busco_dataset_list.txt" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index f8fed1e8..953e9102 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -426,9 +426,9 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -453,6 +453,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index d8ea9618..2043d3e2 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3539,9 +3539,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3557,6 +3557,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json index 69e6a8e3..974250e3 100644 --- a/target/nextflow/busco/busco_run/nextflow_schema.json +++ b/target/nextflow/busco/busco_run/nextflow_schema.json @@ -1,471 +1,287 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "busco_run", -"description": "Assessment of genome assembly and annotation completeness with single copy orthologs", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format", - "help_text": "Type: `file`, required, example: `file.fasta`. Input sequence file in FASTA format. Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set. Also possible to use a path to a directory containing multiple input files.\n" - - } - - - , - "mode": { - "type": - "string", - "description": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run", - "help_text": "Type: `string`, required, example: `proteins`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. Specify which BUSCO analysis mode to run. There are three valid modes:\n - geno or genome, for genome assemblies (DNA)\n - tran or transcriptome, for transcriptome assemblies (DNA)\n - prot or proteins, for annotated gene sets (protein)\n", - "enum": ["genome", "geno", "transcriptome", "tran", "proteins", "prot"] - - - } - - - , - "lineage_dataset": { - "type": - "string", - "description": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", - "help_text": "Type: `string`, example: `stramenopiles_odb10`. Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed. \nThe full list of available datasets can be viewed [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the busco/busco_list_datasets component.\nWhen unsure, the \"--auto_lineage\" flag can be set to automatically find the optimal lineage path.\nBUSCO will automatically download the requested dataset if it is not already present in the download folder. \nYou can optionally provide a path to a local dataset instead of a name, e.g. path/to/dataset.\nDatasets can be downloaded using the busco/busco_download_dataset component.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "short_summary_json": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format", - "help_text": "Type: `file`, default: `$id.$key.short_summary_json.json`, example: `short_summary.json`. Output file for short summary in JSON format.\n" - , - "default":"$id.$key.short_summary_json.json" - } - - - , - "short_summary_txt": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format", - "help_text": "Type: `file`, default: `$id.$key.short_summary_txt.txt`, example: `short_summary.txt`. Output file for short summary in TXT format.\n" - , - "default":"$id.$key.short_summary_txt.txt" - } - - - , - "full_table": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format", - "help_text": "Type: `file`, default: `$id.$key.full_table.tsv`, example: `full_table.tsv`. Full table output in TSV format.\n" - , - "default":"$id.$key.full_table.tsv" - } - - - , - "missing_busco_list": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format", - "help_text": "Type: `file`, default: `$id.$key.missing_busco_list.tsv`, example: `missing_busco_list.tsv`. Missing list output in TSV format.\n" - , - "default":"$id.$key.missing_busco_list.tsv" - } - - - , - "output_dir": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_dir`, example: `output_dir`. The full output directory, if so desired", - "help_text": "Type: `file`, default: `$id.$key.output_dir`, example: `output_dir`. The full output directory, if so desired.\n" - , - "default":"$id.$key.output_dir" - } - - -} -}, - - - "resource and run settings" : { - "title": "Resource and Run Settings", - "type": "object", - "description": "No description", - "properties": { - - - "force": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force rewriting of existing files", - "help_text": "Type: `boolean_true`, default: `false`. Force rewriting of existing files. Must be used when output files with the provided name already exist.\n" - , - "default":false - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors", - "help_text": "Type: `boolean_true`, default: `false`. Disable the info logs, displays only errors.\n" - , - "default":false - } - - - , - "restart": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed", - "help_text": "Type: `boolean_true`, default: `false`. Continue a run that had already partially completed. Restarting skips calls to tools that have completed but performs all pre- and post-processing steps.\n" - , - "default":false - } - - - , - "tar": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space", - "help_text": "Type: `boolean_true`, default: `false`. Compress some subdirectories with many files to save space.\n" - , - "default":false - } - - -} -}, - - - "lineage dataset settings" : { - "title": "Lineage Dataset Settings", - "type": "object", - "description": "No description", - "properties": { - - - "auto_lineage": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", - "help_text": "Type: `boolean_true`, default: `false`. Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.\n" - , - "default":false - } - - - , - "auto_lineage_euk": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path", - "help_text": "Type: `boolean_true`, default: `false`. Run auto-placement just on eukaryota tree to find optimal lineage path.\n" - , - "default":false - } - - - , - "auto_lineage_prok": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path", - "help_text": "Type: `boolean_true`, default: `false`. Run auto_lineage just on prokaryota trees to find optimum lineage path.\n" - , - "default":false - } - - - , - "datasets_version": { - "type": - "string", - "description": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n", - "help_text": "Type: `string`, example: `odb10`. Specify the version of BUSCO datasets\n" - - } - - -} -}, - - - "augustus settings" : { - "title": "Augustus Settings", - "type": "object", - "description": "No description", - "properties": { - - - "augustus": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs", - "help_text": "Type: `boolean_true`, default: `false`. Use augustus gene predictor for eukaryote runs.\n" - , - "default":false - } - - - , - "augustus_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github", - "help_text": "Type: `string`, example: `--PARAM1=VALUE1,--PARAM2=VALUE2`. Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\nParameters should be contained within a single string, without whitespace and seperated by commas.\n" - - } - - - , - "augustus_species": { - "type": - "string", - "description": "Type: `string`. Specify the augustus species\n", - "help_text": "Type: `string`. Specify the augustus species\n" - - } - - - , - "long": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode", - "help_text": "Type: `boolean_true`, default: `false`. Optimize Augustus self-training mode. This adds considerably to the run time, but can improve results for some non-model organisms.\n" - , - "default":false - } - - -} -}, - - - "bbtools settings" : { - "title": "BBTools Settings", - "type": "object", - "description": "No description", - "properties": { - - - "contig_break": { - "type": - "integer", - "description": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis", - "help_text": "Type: `integer`. Number of contiguous Ns to signify a break between contigs in BBTools analysis.\n" - - } - - - , - "limit": { - "type": - "integer", - "description": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO", - "help_text": "Type: `integer`. Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.\nThis option is only effective in pipelines using BLAST, i.e. the genome pipeline (see --augustus) or the prokaryota transcriptome pipeline.\n" - - } - - - , - "scaffold_composition": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition", - "help_text": "Type: `boolean_true`, default: `false`. Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n" - , - "default":false - } - - -} -}, - - - "blast settings" : { - "title": "BLAST Settings", - "type": "object", - "description": "No description", - "properties": { - - - "e_value": { - "type": - "number", - "description": "Type: `double`. E-value cutoff for BLAST searches", - "help_text": "Type: `double`. E-value cutoff for BLAST searches.\n" - - } - - -} -}, - - - "protein gene prediction settings" : { - "title": "Protein Gene Prediction settings", - "type": "object", - "description": "No description", - "properties": { - - - "miniprot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor", - "help_text": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor.\n" - , - "default":false - } - - -} -}, - - - "metaeuk settings" : { - "title": "MetaEuk Settings", - "type": "object", - "description": "No description", - "properties": { - - - "metaeuk": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor", - "help_text": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor.\n" - , - "default":false - } - - - , - "metaeuk_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github", - "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" - - } - - - , - "metaeuk_rerun_parameters": { - "type": - "string", - "description": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github", - "help_text": "Type: `string`, example: `--max-overlap=15,--min-exon-aa=15`. Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "busco_run", + "description": "Assessment of genome assembly and annotation completeness with single copy orthologs", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input sequence file in FASTA format", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"file.fasta\"`. " + }, + "mode": { + "type": "string", + "description": "Specify which BUSCO analysis mode to run", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"proteins\"`, choices: ``genome`, `geno`, `transcriptome`, `tran`, `proteins`, `prot``. ", + "enum": [ + "genome", + "geno", + "transcriptome", + "tran", + "proteins", + "prot" + ] + }, + "lineage_dataset": { + "type": "string", + "description": "Specify a BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed", + "help_text": "Type: `string`, multiple: `False`, example: `\"stramenopiles_odb10\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "short_summary_json": { + "type": "string", + "format": "path", + "description": "Output file for short summary in JSON format.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.short_summary_json.json\"`, direction: `output`, example: `\"short_summary.json\"`. ", + "default": "$id.$key.short_summary_json.json" + }, + "short_summary_txt": { + "type": "string", + "format": "path", + "description": "Output file for short summary in TXT format.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.short_summary_txt.txt\"`, direction: `output`, example: `\"short_summary.txt\"`. ", + "default": "$id.$key.short_summary_txt.txt" + }, + "full_table": { + "type": "string", + "format": "path", + "description": "Full table output in TSV format.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.full_table.tsv\"`, direction: `output`, example: `\"full_table.tsv\"`. ", + "default": "$id.$key.full_table.tsv" + }, + "missing_busco_list": { + "type": "string", + "format": "path", + "description": "Missing list output in TSV format.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.missing_busco_list.tsv\"`, direction: `output`, example: `\"missing_busco_list.tsv\"`. ", + "default": "$id.$key.missing_busco_list.tsv" + }, + "output_dir": { + "type": "string", + "format": "path", + "description": "The full output directory, if so desired.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_dir\"`, direction: `output`, example: `\"output_dir\"`. ", + "default": "$id.$key.output_dir" + } + } }, - - { - "$ref": "#/definitions/resource and run settings" + "resource and run settings": { + "title": "Resource and Run Settings", + "type": "object", + "description": "No description", + "properties": { + "force": { + "type": "boolean", + "description": "Force rewriting of existing files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "quiet": { + "type": "boolean", + "description": "Disable the info logs, displays only errors.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "restart": { + "type": "boolean", + "description": "Continue a run that had already partially completed", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "tar": { + "type": "boolean", + "description": "Compress some subdirectories with many files to save space.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/lineage dataset settings" + "lineage dataset settings": { + "title": "Lineage Dataset Settings", + "type": "object", + "description": "No description", + "properties": { + "auto_lineage": { + "type": "boolean", + "description": "Run auto-lineage pipelilne to automatically determine BUSCO lineage dataset that is most closely related to the assembly or gene set being assessed.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "auto_lineage_euk": { + "type": "boolean", + "description": "Run auto-placement just on eukaryota tree to find optimal lineage path.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "auto_lineage_prok": { + "type": "boolean", + "description": "Run auto_lineage just on prokaryota trees to find optimum lineage path.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "datasets_version": { + "type": "string", + "description": "Specify the version of BUSCO datasets\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"odb10\"`. " + } + } }, - - { - "$ref": "#/definitions/augustus settings" + "augustus settings": { + "title": "Augustus Settings", + "type": "object", + "description": "No description", + "properties": { + "augustus": { + "type": "boolean", + "description": "Use augustus gene predictor for eukaryote runs.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "augustus_parameters": { + "type": "string", + "description": "Additional parameters to be passed to Augustus (see Augustus documentation: https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md).\nParameters should be contained within a single string, without whitespace and seperated by commas.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"--PARAM1=VALUE1,--PARAM2=VALUE2\"`. " + }, + "augustus_species": { + "type": "string", + "description": "Specify the augustus species\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "long": { + "type": "boolean", + "description": "Optimize Augustus self-training mode", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/bbtools settings" + "bbtools settings": { + "title": "BBTools Settings", + "type": "object", + "description": "No description", + "properties": { + "contig_break": { + "type": "integer", + "description": "Number of contiguous Ns to signify a break between contigs in BBTools analysis.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "limit": { + "type": "integer", + "description": "Number of candidate regions (contig or transcript) from the BLAST output to consider per BUSCO.\nThis option is only effective in pipelines using BLAST, i.e", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "scaffold_composition": { + "type": "boolean", + "description": "Writes ACGTN content per scaffold to a file scaffold_composition.txt.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/blast settings" + "blast settings": { + "title": "BLAST Settings", + "type": "object", + "description": "No description", + "properties": { + "e_value": { + "type": "number", + "description": "E-value cutoff for BLAST searches.\n", + "help_text": "Type: `double`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/protein gene prediction settings" + "protein gene prediction settings": { + "title": "Protein Gene Prediction settings", + "type": "object", + "description": "No description", + "properties": { + "miniprot": { + "type": "boolean", + "description": "Use Miniprot gene predictor.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/metaeuk settings" + "metaeuk settings": { + "title": "MetaEuk Settings", + "type": "object", + "description": "No description", + "properties": { + "metaeuk": { + "type": "boolean", + "description": "Use Metaeuk gene predictor.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "metaeuk_parameters": { + "type": "string", + "description": "Pass additional arguments to Metaeuk for the first run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"--max-overlap=15,--min-exon-aa=15\"`. " + }, + "metaeuk_rerun_parameters": { + "type": "string", + "description": "Pass additional arguments to Metaeuk for the second run (see Metaeuk documentation https://github.com/soedinglab/metaeuk).\nAll parameters should be contained within a single string with no white space, with each parameter separated by a comma.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"--max-overlap=15,--min-exon-aa=15\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/resource and run settings" + }, + { + "$ref": "#/$defs/lineage dataset settings" + }, + { + "$ref": "#/$defs/augustus settings" + }, + { + "$ref": "#/$defs/bbtools settings" + }, + { + "$ref": "#/$defs/blast settings" + }, + { + "$ref": "#/$defs/protein gene prediction settings" + }, + { + "$ref": "#/$defs/metaeuk settings" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml index 8b3eaa95..e3a8c8ae 100644 --- a/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_count/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "author" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - name: "Robrecht Cannoodt" roles: - "author" @@ -378,9 +373,9 @@ build_info: output: "target/nextflow/cellranger/cellranger_count" executable: "target/nextflow/cellranger/cellranger_count/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -405,6 +400,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cellranger/cellranger_count/main.nf b/target/nextflow/cellranger/cellranger_count/main.nf index 698c4eee..3650680b 100644 --- a/target/nextflow/cellranger/cellranger_count/main.nf +++ b/target/nextflow/cellranger/cellranger_count/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } }, { @@ -3481,9 +3473,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_count", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3499,6 +3491,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cellranger/cellranger_count/nextflow_schema.json b/target/nextflow/cellranger/cellranger_count/nextflow_schema.json index 65f1d1a8..f8bd5a9a 100644 --- a/target/nextflow/cellranger/cellranger_count/nextflow_schema.json +++ b/target/nextflow/cellranger/cellranger_count/nextflow_schema.json @@ -1,343 +1,206 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "cellranger_count", -"description": "Count gene expression and/or feature barcode reads from a single sample and GEM well\n", -"type": "object", -"definitions": { - - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. The folder to store the alignment results", - "help_text": "Type: `file`, required, default: `$id.$key.output`. The folder to store the alignment results." - , - "default":"$id.$key.output" - } - - - , - "create_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable or disable BAM file generation", - "help_text": "Type: `boolean_true`, default: `false`. Enable or disable BAM file generation. Setting this to false\nreduces the total computation time and the size of the output\ndirectory (BAM file not generated). We recommend setting\nit to true if unsure. See https://10xgen.com/create-bam for\nadditional guidance.\n" - , - "default":false - } - - - , - "no_secondary": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable secondary analysis, e", - "help_text": "Type: `boolean_true`, default: `false`. Disable secondary analysis, e.g. clustering." - , - "default":false - } - - -} -}, - - - "fastq inputs" : { - "title": "FASTQ inputs", - "type": "object", - "description": "No description", - "properties": { - - - "fastqs": { - "type": - "string", - "description": "Type: List of `file`, required, example: `sample_S1_L001_R1_001.fastq.gz;sample_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. The fastq", - "help_text": "Type: List of `file`, required, example: `sample_S1_L001_R1_001.fastq.gz;sample_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. The fastq.gz files to align. Can also be a single directory containing fastq.gz files." - - } - - - , - "description": { - "type": - "string", - "description": "Type: `string`. Sample description to embed in output files", - "help_text": "Type: `string`. Sample description to embed in output files" - - } - - - , - "sample": { - "type": - "string", - "description": "Type: `string`, example: `sample_S1`. Prefix of the filenames of FASTQs to select", - "help_text": "Type: `string`, example: `sample_S1`. Prefix of the filenames of FASTQs to select" - - } - - - , - "lanes": { - "type": - "string", - "description": "Type: List of `integer`, example: `1;2;3`, multiple_sep: `\";\"`. Only use FASTQs from selected lanes", - "help_text": "Type: List of `integer`, example: `1;2;3`, multiple_sep: `\";\"`. Only use FASTQs from selected lanes." - - } - - - , - "libraries": { - "type": - "string", - "description": "Type: `file`, example: `libraries.csv`. CSV file declaring input library data sources", - "help_text": "Type: `file`, example: `libraries.csv`. CSV file declaring input library data sources" - - } - - -} -}, - - - "reference inputs" : { - "title": "Reference inputs", - "type": "object", - "description": "No description", - "properties": { - - - "transcriptome": { - "type": - "string", - "description": "Type: `file`, required, example: `transcriptome.tar.gz`. Path of folder containing 10x-compatible transcriptome reference", - "help_text": "Type: `file`, required, example: `transcriptome.tar.gz`. Path of folder containing 10x-compatible transcriptome reference. Can also be a `.tar.gz` file." - - } - - - , - "feature_ref": { - "type": - "string", - "description": "Type: `file`, example: `feature_ref.csv`. Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes", - "help_text": "Type: `file`, example: `feature_ref.csv`. Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes" - - } - - -} -}, - - - "analysis settings" : { - "title": "Analysis settings", - "type": "object", - "description": "No description", - "properties": { - - - "expect_cells": { - "type": - "integer", - "description": "Type: `integer`. Expected number of recovered cells, used as input to cell calling algorithm", - "help_text": "Type: `integer`. Expected number of recovered cells, used as input to cell calling algorithm." - - } - - - , - "force_cells": { - "type": - "integer", - "description": "Type: `integer`. Force pipeline to use this number of cells, bypassing cell calling algorithm", - "help_text": "Type: `integer`. Force pipeline to use this number of cells, bypassing cell calling algorithm. Minimum: 10.\n" - - } - - - , - "r1_length": { - "type": - "integer", - "description": "Type: `integer`. Hard trim the input Read 1 to this length before analysis", - "help_text": "Type: `integer`. Hard trim the input Read 1 to this length before analysis" - - } - - - , - "r2_length": { - "type": - "integer", - "description": "Type: `integer`. Hard trim the input Read 2 to this length before analysis", - "help_text": "Type: `integer`. Hard trim the input Read 2 to this length before analysis" - - } - - - , - "include_introns": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Include intronic reads in count", - "help_text": "Type: `boolean_true`, default: `false`. Include intronic reads in count. Default: true." - , - "default":false - } - - - , - "chemistry": { - "type": - "string", - "description": "Type: `string`, example: `auto`. Assay configuration", - "help_text": "Type: `string`, example: `auto`. Assay configuration.\n\nNOTE: by default the assay configuration is detected automatically, which is the recommended mode. You usually will not need to specify a chemistry. \n\nOptions are:\n\n- `\u0027auto\u0027` for autodetection\n- `\u0027threeprime\u0027` for Single Cell 3\u0027\n- `\u0027fiveprime\u0027` for Single Cell 5\u0027\n- `\u0027SC3Pv1\u0027` or `\u0027SC3Pv2\u0027` or `\u0027SC3Pv3\u0027` or `\u0027SC3Pv4\u0027` for\nSingle Cell 3\u0027 v1/v2/v3/v4\n- `\u0027SC3Pv3LT\u0027` for Single Cell 3\u0027 v3 LT\n- `\u0027SC3Pv3HT\u0027` for Single Cell 3\u0027 v3 HT\n- `\u0027SC5P-PE\u0027` or `\u0027SC5P-PE-v3\u0027` or `\u0027SC5P-R2\u0027` or `\u0027SC5P-R2-v3\u0027` for Single Cell 5\u0027, paired-end/R2-only\n- `\u0027SC-FB\u0027` for Single Cell Antibody-only 3\u0027 v2 or 5\u0027\n\nTo analyze the GEX portion of multiome data, chemistry must be set to `\u0027ARC-v1\u0027`.\n\nSee the [10x Genomics FAQ](https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-) for more information on how chemistry is detected.\n" - - } - - - , - "cell_annotation_model": { - "type": - "string", - "description": "Type: `string`. Cell annotation model to use", - "help_text": "Type: `string`. Cell annotation model to use. Valid model names can be viewed by\nrunning `cellranger cloud annotation models` or on the\n[10x Genomics Support site](https://www.10xgenomics.com/support).\n\nIf \"auto\", uses the default model for the species.\nIf not provided, does not run cell annotation.\n" - - } - - - , - "min_crispr_umi": { - "type": - "integer", - "description": "Type: `integer`. Minimum CRISPR UMI threshold", - "help_text": "Type: `integer`. Minimum CRISPR UMI threshold. Default: 3.\n" - - } - - -} -}, - - - "additional arguments" : { - "title": "Additional arguments", - "type": "object", - "description": "No description", - "properties": { - - - "no_libraries": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the \u0027libraries\u0027 flag", - "help_text": "Type: `boolean_true`, default: `false`. Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the \u0027libraries\u0027 flag.\n" - , - "default":false - } - - - , - "check_library_compatibility": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Whether to check for barcode compatibility between libraries", - "help_text": "Type: `boolean_true`, default: `false`. Whether to check for barcode compatibility between libraries.\n" - , - "default":false - } - - - , - "tenx_cloud_token": { - "type": - "string", - "description": "Type: `file`. The path to the 10x Cloud Analysis user token used to enable cell\nannotation", - "help_text": "Type: `file`. The path to the 10x Cloud Analysis user token used to enable cell\nannotation. If not provided, will default to the location stored\nthrough cellranger cloud auth setup.\n" - - } - - - , - "dry": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not execute the pipeline", - "help_text": "Type: `boolean_true`, default: `false`. Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/outputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "cellranger_count", + "description": "Count gene expression and/or feature barcode reads from a single sample and GEM well\n", + "type": "object", + "$defs": { + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The folder to store the alignment results.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + }, + "create_bam": { + "type": "boolean", + "description": "Enable or disable BAM file generation", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_secondary": { + "type": "boolean", + "description": "Disable secondary analysis, e.g", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/fastq inputs" + "fastq inputs": { + "title": "FASTQ inputs", + "type": "object", + "description": "No description", + "properties": { + "fastqs": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "The fastq.gz files to align", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample_S1_L001_R1_001.fastq.gz\";\"sample_S1_L001_R2_001.fastq.gz\"]`. " + }, + "description": { + "type": "string", + "description": "Sample description to embed in output files", + "help_text": "Type: `string`, multiple: `False`. " + }, + "sample": { + "type": "string", + "description": "Prefix of the filenames of FASTQs to select", + "help_text": "Type: `string`, multiple: `False`, example: `\"sample_S1\"`. " + }, + "lanes": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Only use FASTQs from selected lanes.", + "help_text": "Type: `integer`, multiple: `True`, example: `[1;2;3]`. " + }, + "libraries": { + "type": "string", + "format": "path", + "description": "CSV file declaring input library data sources", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"libraries.csv\"`. " + } + } }, - - { - "$ref": "#/definitions/reference inputs" + "reference inputs": { + "title": "Reference inputs", + "type": "object", + "description": "No description", + "properties": { + "transcriptome": { + "type": "string", + "format": "path", + "exists": true, + "description": "Path of folder containing 10x-compatible transcriptome reference", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome.tar.gz\"`. " + }, + "feature_ref": { + "type": "string", + "format": "path", + "description": "Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"feature_ref.csv\"`. " + } + } }, - - { - "$ref": "#/definitions/analysis settings" + "analysis settings": { + "title": "Analysis settings", + "type": "object", + "description": "No description", + "properties": { + "expect_cells": { + "type": "integer", + "description": "Expected number of recovered cells, used as input to cell calling algorithm.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "force_cells": { + "type": "integer", + "description": "Force pipeline to use this number of cells, bypassing cell calling algorithm", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "r1_length": { + "type": "integer", + "description": "Hard trim the input Read 1 to this length before analysis", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "r2_length": { + "type": "integer", + "description": "Hard trim the input Read 2 to this length before analysis", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "include_introns": { + "type": "boolean", + "description": "Include intronic reads in count", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chemistry": { + "type": "string", + "description": "Assay configuration.\n\nNOTE: by default the assay configuration is detected automatically, which is the recommended mode", + "help_text": "Type: `string`, multiple: `False`, example: `\"auto\"`. " + }, + "cell_annotation_model": { + "type": "string", + "description": "Cell annotation model to use", + "help_text": "Type: `string`, multiple: `False`. " + }, + "min_crispr_umi": { + "type": "integer", + "description": "Minimum CRISPR UMI threshold", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/additional arguments" + "additional arguments": { + "title": "Additional arguments", + "type": "object", + "description": "No description", + "properties": { + "no_libraries": { + "type": "boolean", + "description": "Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the 'libraries' flag.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "check_library_compatibility": { + "type": "boolean", + "description": "Whether to check for barcode compatibility between libraries.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "tenx_cloud_token": { + "type": "string", + "format": "path", + "description": "The path to the 10x Cloud Analysis user token used to enable cell\nannotation", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "dry": { + "type": "boolean", + "description": "Do not execute the pipeline", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/fastq inputs" + }, + { + "$ref": "#/$defs/reference inputs" + }, + { + "$ref": "#/$defs/analysis settings" + }, + { + "$ref": "#/$defs/additional arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml index ee25ad6b..b7a689b8 100644 --- a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "author" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Arguments" arguments: @@ -198,9 +193,9 @@ build_info: output: "target/nextflow/cellranger/cellranger_mkref" executable: "target/nextflow/cellranger/cellranger_mkref/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -225,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cellranger/cellranger_mkref/main.nf b/target/nextflow/cellranger/cellranger_mkref/main.nf index b5123a01..58055e98 100644 --- a/target/nextflow/cellranger/cellranger_mkref/main.nf +++ b/target/nextflow/cellranger/cellranger_mkref/main.nf @@ -3044,17 +3044,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3289,9 +3281,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_mkref", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3307,6 +3299,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json index c1069571..58971ff1 100644 --- a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json +++ b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json @@ -1,101 +1,61 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "cellranger_mkref", -"description": "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files.", -"type": "object", -"definitions": { - - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "genome_fasta": { - "type": - "string", - "description": "Type: `file`, required, example: `genome_sequence.fa.gz`. Reference genome fasta", - "help_text": "Type: `file`, required, example: `genome_sequence.fa.gz`. Reference genome fasta." - - } - - - , - "transcriptome_gtf": { - "type": - "string", - "description": "Type: `file`, required, example: `transcriptome_annotation.gtf.gz`. Reference transcriptome annotation", - "help_text": "Type: `file`, required, example: `transcriptome_annotation.gtf.gz`. Reference transcriptome annotation." - - } - - - , - "reference_version": { - "type": - "string", - "description": "Type: `string`. Optional reference version string to include with reference", - "help_text": "Type: `string`. Optional reference version string to include with reference" - - } - - - , - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`, example: `cellranger_reference`. Output folder", - "help_text": "Type: `file`, required, default: `$id.$key.output`, example: `cellranger_reference`. Output folder" - , - "default":"$id.$key.output" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "cellranger_mkref", + "description": "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files.", + "type": "object", + "$defs": { + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "genome_fasta": { + "type": "string", + "format": "path", + "exists": true, + "description": "Reference genome fasta.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genome_sequence.fa.gz\"`. " + }, + "transcriptome_gtf": { + "type": "string", + "format": "path", + "exists": true, + "description": "Reference transcriptome annotation.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome_annotation.gtf.gz\"`. " + }, + "reference_version": { + "type": "string", + "description": "Optional reference version string to include with reference", + "help_text": "Type: `string`, multiple: `False`. " + }, + "output": { + "type": "string", + "format": "path", + "description": "Output folder", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"cellranger_reference\"`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index bce0c368..f01887b4 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -743,9 +743,9 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -770,6 +770,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index acc5d182..06856515 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3849,9 +3849,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3867,6 +3867,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/cutadapt/nextflow_schema.json b/target/nextflow/cutadapt/nextflow_schema.json index 2b7fb1b4..6293724d 100644 --- a/target/nextflow/cutadapt/nextflow_schema.json +++ b/target/nextflow/cutadapt/nextflow_schema.json @@ -1,775 +1,488 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "cutadapt", -"description": "Cutadapt removes adapter sequences from high-throughput sequencing reads.\n", -"type": "object", -"definitions": { - - - - "specify adapters for r1" : { - "title": "Specify Adapters for R1", - "type": "object", - "description": "No description", - "properties": { - - - "adapter": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n" - - } - - - , - "front": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n" - - } - - - , - "anywhere": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n" - - } - - -} -}, - - - "specify adapters using fasta files for r1" : { - "title": "Specify Adapters using Fasta files for R1", - "type": "object", - "description": "No description", - "properties": { - - - "adapter_fasta": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n" - - } - - - , - "front_fasta": { - "type": - "string", - "description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)", - "help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n" - - } - - - , - "anywhere_fasta": { - "type": - "string", - "description": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)", - "help_text": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n" - - } - - -} -}, - - - "specify adapters for r2" : { - "title": "Specify Adapters for R2", - "type": "object", - "description": "No description", - "properties": { - - - "adapter_r2": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n" - - } - - - , - "front_r2": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n" - - } - - - , - "anywhere_r2": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Sequence of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n" - - } - - -} -}, - - - "specify adapters using fasta files for r2" : { - "title": "Specify Adapters using Fasta files for R2", - "type": "object", - "description": "No description", - "properties": { - - - "adapter_r2_fasta": { - "type": - "string", - "description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read)", - "help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 3\u0027 end (paired data:\nof the first read). The adapter and subsequent bases are\ntrimmed. If a \u0027$\u0027 character is appended (\u0027anchoring\u0027), the\nadapter is only found if it is a suffix of the read.\n" - - } - - - , - "front_r2_fasta": { - "type": - "string", - "description": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read)", - "help_text": "Type: `file`. Fasta file containing sequences of an adapter ligated to the 5\u0027 end (paired data:\nof the first read). The adapter and any preceding bases\nare trimmed. Partial matches at the 5\u0027 end are allowed. If\na \u0027^\u0027 character is prepended (\u0027anchoring\u0027), the adapter is\nonly found if it is a prefix of the read.\n" - - } - - - , - "anywhere_r2_fasta": { - "type": - "string", - "description": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read)", - "help_text": "Type: `file`. Fasta file containing sequences of an adapter that may be ligated to the 5\u0027 or 3\u0027\nend (paired data: of the first read). Both types of\nmatches as described under -a and -g are allowed. If the\nfirst base of the read is part of the match, the behavior\nis as with -g, otherwise as with -a. This option is mostly\nfor rescuing failed library preparations - do not use if\nyou know which end your adapter was ligated to!\n" - - } - - -} -}, - - - "paired-end options" : { - "title": "Paired-end options", - "type": "object", - "description": "No description", - "properties": { - - - "pair_adapters": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Treat adapters given with -a/-A etc", - "help_text": "Type: `boolean_true`, default: `false`. Treat adapters given with -a/-A etc. as pairs. Either both\nor none are removed from each read pair.\n" - , - "default":false - } - - - , - "pair_filter": { - "type": - "string", - "description": "Type: `string`, choices: ``any`, `both`, `first``. Which of the reads in a paired-end read have to match the\nfiltering criterion in order for the pair to be filtered", - "help_text": "Type: `string`, choices: ``any`, `both`, `first``. Which of the reads in a paired-end read have to match the\nfiltering criterion in order for the pair to be filtered.\n", - "enum": ["any", "both", "first"] - - - } - - - , - "interleaved": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Read and/or write interleaved paired-end reads", - "help_text": "Type: `boolean_true`, default: `false`. Read and/or write interleaved paired-end reads.\n" - , - "default":false - } - - -} -}, - - - "input parameters" : { - "title": "Input parameters", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input fastq file for single-end reads or R1 for paired-end reads", - "help_text": "Type: `file`, required. Input fastq file for single-end reads or R1 for paired-end reads.\n" - - } - - - , - "input_r2": { - "type": - "string", - "description": "Type: `file`. Input fastq file for R2 in the case of paired-end reads", - "help_text": "Type: `file`. Input fastq file for R2 in the case of paired-end reads.\n" - - } - - - , - "error_rate": { - "type": - "number", - "description": "Type: `double`, example: `0.1`. Maximum allowed error rate (if 0 \u003c= E \u003c 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger \u003e= 1)", - "help_text": "Type: `double`, example: `0.1`. Maximum allowed error rate (if 0 \u003c= E \u003c 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger \u003e= 1). Error rate = no. of errors divided by\nlength of matching region. Default: 0.1 (10%).\n" - - } - - - , - "no_indels": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Allow only mismatches in alignments", - "help_text": "Type: `boolean_true`, default: `false`. Allow only mismatches in alignments.\n" - , - "default":false - } - - - , - "times": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Remove up to COUNT adapters from each read", - "help_text": "Type: `integer`, example: `1`. Remove up to COUNT adapters from each read. Default: 1.\n" - - } - - - , - "overlap": { - "type": - "integer", - "description": "Type: `integer`, example: `3`. Require MINLENGTH overlap between read and adapter for an\nadapter to be found", - "help_text": "Type: `integer`, example: `3`. Require MINLENGTH overlap between read and adapter for an\nadapter to be found. The default is 3.\n" - - } - - - , - "match_read_wildcards": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Interpret IUPAC wildcards in reads", - "help_text": "Type: `boolean_true`, default: `false`. Interpret IUPAC wildcards in reads.\n" - , - "default":false - } - - - , - "no_match_adapter_wildcards": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not interpret IUPAC wildcards in adapters", - "help_text": "Type: `boolean_true`, default: `false`. Do not interpret IUPAC wildcards in adapters.\n" - , - "default":false - } - - - , - "action": { - "type": - "string", - "description": "Type: `string`, example: `trim`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. What to do if a match was found", - "help_text": "Type: `string`, example: `trim`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. What to do if a match was found. trim: trim adapter and\nup- or downstream sequence; retain: trim, but retain\nadapter; mask: replace with \u0027N\u0027 characters; lowercase:\nconvert to lowercase; none: leave unchanged.\nThe default is trim.\n", - "enum": ["trim", "retain", "mask", "lowercase", "none"] - - - } - - - , - "revcomp": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Check both the read and its reverse complement for adapter\nmatches", - "help_text": "Type: `boolean_true`, default: `false`. Check both the read and its reverse complement for adapter\nmatches. If match is on reverse-complemented version,\noutput that one.\n" - , - "default":false - } - - -} -}, - - - "demultiplexing options" : { - "title": "Demultiplexing options", - "type": "object", - "description": "No description", - "properties": { - - - "demultiplex_mode": { - "type": - "string", - "description": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it", - "help_text": "Type: `string`, choices: ``single`, `unique_dual`, `combinatorial_dual``. Enable demultiplexing and set the mode for it.\nWith mode \u0027unique_dual\u0027, adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs. This implies\n--pair_adapters.\nEnabling mode \u0027combinatorial_dual\u0027 allows all combinations of the sets of indexes\non R1 and R2. It is necessary to write each read pair to an output\nfile depending on the adapters found on both R1 and R2.\nMode \u0027single\u0027, uses indexes or barcodes located at the 5\u0027\nend of the R1 read (single). \n", - "enum": ["single", "unique_dual", "combinatorial_dual"] - - - } - - -} -}, - - - "read modifications" : { - "title": "Read modifications", - "type": "object", - "description": "No description", - "properties": { - - - "cut": { - "type": - "string", - "description": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2)", - "help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2). If LEN is positive, remove bases from the\nbeginning. If LEN is negative, remove bases from the end.\nCan be used twice if LENs have different signs. Applied\n*before* adapter trimming.\n" - - } - - - , - "cut_r2": { - "type": - "string", - "description": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (for R2)", - "help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Remove LEN bases from each read (for R2). If LEN is positive, remove bases from the\nbeginning. If LEN is negative, remove bases from the end.\nCan be used twice if LENs have different signs. Applied\n*before* adapter trimming.\n" - - } - - - , - "nextseq_trim": { - "type": - "string", - "description": "Type: `string`. NextSeq-specific quality trimming (each read)", - "help_text": "Type: `string`. NextSeq-specific quality trimming (each read). Trims also\ndark cycles appearing as high-quality G bases.\n" - - } - - - , - "quality_cutoff": { - "type": - "string", - "description": "Type: `string`. Trim low-quality bases from 5\u0027 and/or 3\u0027 ends of each read\nbefore adapter removal", - "help_text": "Type: `string`. Trim low-quality bases from 5\u0027 and/or 3\u0027 ends of each read\nbefore adapter removal. Applied to both reads if data is\npaired. If one value is given, only the 3\u0027 end is trimmed.\nIf two comma-separated cutoffs are given, the 5\u0027 end is\ntrimmed with the first cutoff, the 3\u0027 end with the second.\n" - - } - - - , - "quality_cutoff_r2": { - "type": - "string", - "description": "Type: `string`. Quality-trimming cutoff for R2", - "help_text": "Type: `string`. Quality-trimming cutoff for R2. Default: same as for R1\n" - - } - - - , - "quality_base": { - "type": - "integer", - "description": "Type: `integer`, example: `33`. Assume that quality values in FASTQ are encoded as\nascii(quality + N)", - "help_text": "Type: `integer`, example: `33`. Assume that quality values in FASTQ are encoded as\nascii(quality + N). This needs to be set to 64 for some\nold Illumina FASTQ files. The default is 33.\n" - - } - - - , - "poly_a": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Trim poly-A tails", - "help_text": "Type: `boolean_true`, default: `false`. Trim poly-A tails" - , - "default":false - } - - - , - "length": { - "type": - "integer", - "description": "Type: `integer`. Shorten reads to LENGTH", - "help_text": "Type: `integer`. Shorten reads to LENGTH. Positive values remove bases at\nthe end while negative ones remove bases at the beginning.\nThis and the following modifications are applied after\nadapter trimming.\n" - - } - - - , - "trim_n": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Trim N\u0027s on ends of reads", - "help_text": "Type: `boolean_true`, default: `false`. Trim N\u0027s on ends of reads." - , - "default":false - } - - - , - "length_tag": { - "type": - "string", - "description": "Type: `string`, example: `length=`. Search for TAG followed by a decimal number in the\ndescription field of the read", - "help_text": "Type: `string`, example: `length=`. Search for TAG followed by a decimal number in the\ndescription field of the read. Replace the decimal number\nwith the correct length of the trimmed read. For example,\nuse --length-tag \u0027length=\u0027 to correct fields like\n\u0027length=123\u0027.\n" - - } - - - , - "strip_suffix": { - "type": - "string", - "description": "Type: `string`. Remove this suffix from read names if present", - "help_text": "Type: `string`. Remove this suffix from read names if present. Can be\ngiven multiple times.\n" - - } - - - , - "prefix": { - "type": - "string", - "description": "Type: `string`. Add this prefix to read names", - "help_text": "Type: `string`. Add this prefix to read names. Use {name} to insert the\nname of the matching adapter.\n" - - } - - - , - "suffix": { - "type": - "string", - "description": "Type: `string`. Add this suffix to read names; can also include {name}\n", - "help_text": "Type: `string`. Add this suffix to read names; can also include {name}\n" - - } - - - , - "rename": { - "type": - "string", - "description": "Type: `string`. Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc", - "help_text": "Type: `string`. Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc. (see documentation)\n" - - } - - - , - "zero_cap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Change negative quality values to zero", - "help_text": "Type: `boolean_true`, default: `false`. Change negative quality values to zero." - , - "default":false - } - - -} -}, - - - "filtering of processed reads" : { - "title": "Filtering of processed reads", - "type": "object", - "description": "Filters are applied after above read modifications. Paired-end reads are\nalways discarded pairwise (see also --pair_filter).\n", - "properties": { - - - "minimum_length": { - "type": - "string", - "description": "Type: `string`, example: `0`. Discard reads shorter than LEN", - "help_text": "Type: `string`, example: `0`. Discard reads shorter than LEN. Default is 0.\nWhen trimming paired-end reads, the minimum lengths for R1 and R2 can be specified separately by separating them with a colon (:).\nIf the colon syntax is not used, the same minimum length applies to both reads, as discussed above.\nAlso, one of the values can be omitted to impose no restrictions.\nFor example, with -m 17:, the length of R1 must be at least 17, but the length of R2 is ignored.\n" - - } - - - , - "maximum_length": { - "type": - "string", - "description": "Type: `string`. Discard reads longer than LEN", - "help_text": "Type: `string`. Discard reads longer than LEN. Default: no limit.\nFor paired reads, see the remark for --minimum_length\n" - - } - - - , - "max_n": { - "type": - "string", - "description": "Type: `string`. Discard reads with more than COUNT \u0027N\u0027 bases", - "help_text": "Type: `string`. Discard reads with more than COUNT \u0027N\u0027 bases. If COUNT is\na number between 0 and 1, it is interpreted as a fraction\nof the read length.\n" - - } - - - , - "max_expected_errors": { - "type": - "string", - "description": "Type: `long`. Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS", - "help_text": "Type: `long`. Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS.\n" - - } - - - , - "max_average_error_rate": { - "type": - "string", - "description": "Type: `long`. as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length", - "help_text": "Type: `long`. as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length.\n" - - } - - - , - "discard_trimmed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard reads that contain an adapter", - "help_text": "Type: `boolean_true`, default: `false`. Discard reads that contain an adapter. Use also -O to\navoid discarding too many randomly matching reads.\n" - , - "default":false - } - - - , - "discard_untrimmed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard reads that do not contain an adapter", - "help_text": "Type: `boolean_true`, default: `false`. Discard reads that do not contain an adapter.\n" - , - "default":false - } - - - , - "discard_casava": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard reads that did not pass CASAVA filtering (header\nhas :Y:)", - "help_text": "Type: `boolean_true`, default: `false`. Discard reads that did not pass CASAVA filtering (header\nhas :Y:).\n" - , - "default":false - } - - -} -}, - - - "output parameters" : { - "title": "Output parameters", - "type": "object", - "description": "No description", - "properties": { - - - "report": { - "type": - "string", - "description": "Type: `string`, example: `full`, choices: ``full`, `minimal``. Which type of report to print: \u0027full\u0027 (default) or \u0027minimal\u0027", - "help_text": "Type: `string`, example: `full`, choices: ``full`, `minimal``. Which type of report to print: \u0027full\u0027 (default) or \u0027minimal\u0027.\n", - "enum": ["full", "minimal"] - - - } - - - , - "json": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write report in JSON format to this file", - "help_text": "Type: `boolean_true`, default: `false`. Write report in JSON format to this file.\n" - , - "default":false - } - - - , - "output": { - "type": - "string", - "description": "Type: List of `file`, required, default: `$id.$key.output_*.fast[a,q]`, example: `fastq/*_001.fast[a,q]`, multiple_sep: `\";\"`. Glob pattern for matching the expected output files", - "help_text": "Type: List of `file`, required, default: `$id.$key.output_*.fast[a,q]`, example: `fastq/*_001.fast[a,q]`, multiple_sep: `\";\"`. Glob pattern for matching the expected output files.\nShould include `$output_dir`.\n" - , - "default":"$id.$key.output_*.fast[a,q]" - } - - - , - "fasta": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output FASTA to standard output even on FASTQ input", - "help_text": "Type: `boolean_true`, default: `false`. Output FASTA to standard output even on FASTQ input.\n" - , - "default":false - } - - - , - "info_file": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write information about each read and its adapter matches\ninto info", - "help_text": "Type: `boolean_true`, default: `false`. Write information about each read and its adapter matches\ninto info.txt in the output directory.\nSee the documentation for the file format.\n" - , - "default":false - } - - -} -}, - - - "debug" : { - "title": "Debug", - "type": "object", - "description": "No description", - "properties": { - - - "debug": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Print debug information", - "help_text": "Type: `boolean_true`, default: `false`. Print debug information" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/specify adapters for r1" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "cutadapt", + "description": "Cutadapt removes adapter sequences from high-throughput sequencing reads.\n", + "type": "object", + "$defs": { + "specify adapters for r1": { + "title": "Specify Adapters for R1", + "type": "object", + "description": "No description", + "properties": { + "adapter": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter ligated to the 3' end (paired data:\nof the first read)", + "help_text": "Type: `string`, multiple: `True`. " + }, + "front": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter ligated to the 5' end (paired data:\nof the first read)", + "help_text": "Type: `string`, multiple: `True`. " + }, + "anywhere": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)", + "help_text": "Type: `string`, multiple: `True`. " + } + } }, - - { - "$ref": "#/definitions/specify adapters using fasta files for r1" + "specify adapters using fasta files for r1": { + "title": "Specify Adapters using Fasta files for R1", + "type": "object", + "description": "No description", + "properties": { + "adapter_fasta": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Fasta file containing sequences of an adapter ligated to the 3' end (paired data:\nof the first read)", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "front_fasta": { + "type": "string", + "format": "path", + "description": "Fasta file containing sequences of an adapter ligated to the 5' end (paired data:\nof the first read)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "anywhere_fasta": { + "type": "string", + "format": "path", + "description": "Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/specify adapters for r2" + "specify adapters for r2": { + "title": "Specify Adapters for R2", + "type": "object", + "description": "No description", + "properties": { + "adapter_r2": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter ligated to the 3' end (paired data:\nof the first read)", + "help_text": "Type: `string`, multiple: `True`. " + }, + "front_r2": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter ligated to the 5' end (paired data:\nof the first read)", + "help_text": "Type: `string`, multiple: `True`. " + }, + "anywhere_r2": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Sequence of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)", + "help_text": "Type: `string`, multiple: `True`. " + } + } }, - - { - "$ref": "#/definitions/specify adapters using fasta files for r2" + "specify adapters using fasta files for r2": { + "title": "Specify Adapters using Fasta files for R2", + "type": "object", + "description": "No description", + "properties": { + "adapter_r2_fasta": { + "type": "string", + "format": "path", + "description": "Fasta file containing sequences of an adapter ligated to the 3' end (paired data:\nof the first read)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "front_r2_fasta": { + "type": "string", + "format": "path", + "description": "Fasta file containing sequences of an adapter ligated to the 5' end (paired data:\nof the first read)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "anywhere_r2_fasta": { + "type": "string", + "format": "path", + "description": "Fasta file containing sequences of an adapter that may be ligated to the 5' or 3'\nend (paired data: of the first read)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/paired-end options" + "paired-end options": { + "title": "Paired-end options", + "type": "object", + "description": "No description", + "properties": { + "pair_adapters": { + "type": "boolean", + "description": "Treat adapters given with -a/-A etc", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "pair_filter": { + "type": "string", + "description": "Which of the reads in a paired-end read have to match the\nfiltering criterion in order for the pair to be filtered.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``any`, `both`, `first``. ", + "enum": [ + "any", + "both", + "first" + ] + }, + "interleaved": { + "type": "boolean", + "description": "Read and/or write interleaved paired-end reads.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/input parameters" + "input parameters": { + "title": "Input parameters", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input fastq file for single-end reads or R1 for paired-end reads.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "input_r2": { + "type": "string", + "format": "path", + "description": "Input fastq file for R2 in the case of paired-end reads.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "error_rate": { + "type": "number", + "description": "Maximum allowed error rate (if 0 <= E < 1), or absolute\nnumber of errors for full-length adapter match (if E is an\ninteger >= 1)", + "help_text": "Type: `double`, multiple: `False`, example: `0.1`. " + }, + "no_indels": { + "type": "boolean", + "description": "Allow only mismatches in alignments.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "times": { + "type": "integer", + "description": "Remove up to COUNT adapters from each read", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "overlap": { + "type": "integer", + "description": "Require MINLENGTH overlap between read and adapter for an\nadapter to be found", + "help_text": "Type: `integer`, multiple: `False`, example: `3`. " + }, + "match_read_wildcards": { + "type": "boolean", + "description": "Interpret IUPAC wildcards in reads.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_match_adapter_wildcards": { + "type": "boolean", + "description": "Do not interpret IUPAC wildcards in adapters.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "action": { + "type": "string", + "description": "What to do if a match was found", + "help_text": "Type: `string`, multiple: `False`, example: `\"trim\"`, choices: ``trim`, `retain`, `mask`, `lowercase`, `none``. ", + "enum": [ + "trim", + "retain", + "mask", + "lowercase", + "none" + ] + }, + "revcomp": { + "type": "boolean", + "description": "Check both the read and its reverse complement for adapter\nmatches", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/demultiplexing options" + "demultiplexing options": { + "title": "Demultiplexing options", + "type": "object", + "description": "No description", + "properties": { + "demultiplex_mode": { + "type": "string", + "description": "Enable demultiplexing and set the mode for it.\nWith mode 'unique_dual', adapters from the first and second read are used,\nand the indexes from the reads are only used in pairs", + "help_text": "Type: `string`, multiple: `False`, choices: ``single`, `unique_dual`, `combinatorial_dual``. ", + "enum": [ + "single", + "unique_dual", + "combinatorial_dual" + ] + } + } }, - - { - "$ref": "#/definitions/read modifications" + "read modifications": { + "title": "Read modifications", + "type": "object", + "description": "No description", + "properties": { + "cut": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Remove LEN bases from each read (or R1 if paired; use --cut_r2\noption for R2)", + "help_text": "Type: `integer`, multiple: `True`. " + }, + "cut_r2": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Remove LEN bases from each read (for R2)", + "help_text": "Type: `integer`, multiple: `True`. " + }, + "nextseq_trim": { + "type": "string", + "description": "NextSeq-specific quality trimming (each read)", + "help_text": "Type: `string`, multiple: `False`. " + }, + "quality_cutoff": { + "type": "string", + "description": "Trim low-quality bases from 5' and/or 3' ends of each read\nbefore adapter removal", + "help_text": "Type: `string`, multiple: `False`. " + }, + "quality_cutoff_r2": { + "type": "string", + "description": "Quality-trimming cutoff for R2", + "help_text": "Type: `string`, multiple: `False`. " + }, + "quality_base": { + "type": "integer", + "description": "Assume that quality values in FASTQ are encoded as\nascii(quality + N)", + "help_text": "Type: `integer`, multiple: `False`, example: `33`. " + }, + "poly_a": { + "type": "boolean", + "description": "Trim poly-A tails", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "length": { + "type": "integer", + "description": "Shorten reads to LENGTH", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "trim_n": { + "type": "boolean", + "description": "Trim N's on ends of reads.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "length_tag": { + "type": "string", + "description": "Search for TAG followed by a decimal number in the\ndescription field of the read", + "help_text": "Type: `string`, multiple: `False`, example: `\"length=\"`. " + }, + "strip_suffix": { + "type": "string", + "description": "Remove this suffix from read names if present", + "help_text": "Type: `string`, multiple: `False`. " + }, + "prefix": { + "type": "string", + "description": "Add this prefix to read names", + "help_text": "Type: `string`, multiple: `False`. " + }, + "suffix": { + "type": "string", + "description": "Add this suffix to read names; can also include {name}\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "rename": { + "type": "string", + "description": "Rename reads using TEMPLATE containing variables such as\n{id}, {adapter_name} etc", + "help_text": "Type: `string`, multiple: `False`. " + }, + "zero_cap": { + "type": "boolean", + "description": "Change negative quality values to zero.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/filtering of processed reads" + "filtering of processed reads": { + "title": "Filtering of processed reads", + "type": "object", + "description": "Filters are applied after above read modifications. Paired-end reads are\nalways discarded pairwise (see also --pair_filter).\n", + "properties": { + "minimum_length": { + "type": "string", + "description": "Discard reads shorter than LEN", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. " + }, + "maximum_length": { + "type": "string", + "description": "Discard reads longer than LEN", + "help_text": "Type: `string`, multiple: `False`. " + }, + "max_n": { + "type": "string", + "description": "Discard reads with more than COUNT 'N' bases", + "help_text": "Type: `string`, multiple: `False`. " + }, + "max_expected_errors": { + "type": "string", + "description": "Discard reads whose expected number of errors (computed\nfrom quality values) exceeds ERRORS.\n", + "help_text": "Type: `long`, multiple: `False`. " + }, + "max_average_error_rate": { + "type": "string", + "description": "as --max_expected_errors (see above), but divided by\nlength to account for reads of varying length.\n", + "help_text": "Type: `long`, multiple: `False`. " + }, + "discard_trimmed": { + "type": "boolean", + "description": "Discard reads that contain an adapter", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "discard_untrimmed": { + "type": "boolean", + "description": "Discard reads that do not contain an adapter.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "discard_casava": { + "type": "boolean", + "description": "Discard reads that did not pass CASAVA filtering (header\nhas :Y:).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/output parameters" + "output parameters": { + "title": "Output parameters", + "type": "object", + "description": "No description", + "properties": { + "report": { + "type": "string", + "description": "Which type of report to print: 'full' (default) or 'minimal'.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"full\"`, choices: ``full`, `minimal``. ", + "enum": [ + "full", + "minimal" + ] + }, + "json": { + "type": "boolean", + "description": "Write report in JSON format to this file.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Glob pattern for matching the expected output files.\nShould include `$output_dir`.\n", + "help_text": "Type: `file`, multiple: `True`, required, default: `\"$id.$key.output_*.fast[a,q]\"`, direction: `output`, example: `[\"fastq/*_001.fast[a,q]\"]`. ", + "default": "$id.$key.output_*.fast[a,q]" + }, + "fasta": { + "type": "boolean", + "description": "Output FASTA to standard output even on FASTQ input.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "info_file": { + "type": "boolean", + "description": "Write information about each read and its adapter matches\ninto info.txt in the output directory.\nSee the documentation for the file format.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/debug" + "debug": { + "title": "Debug", + "type": "object", + "description": "No description", + "properties": { + "debug": { + "type": "boolean", + "description": "Print debug information", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/specify adapters for r1" + }, + { + "$ref": "#/$defs/specify adapters using fasta files for r1" + }, + { + "$ref": "#/$defs/specify adapters for r2" + }, + { + "$ref": "#/$defs/specify adapters using fasta files for r2" + }, + { + "$ref": "#/$defs/paired-end options" + }, + { + "$ref": "#/$defs/input parameters" + }, + { + "$ref": "#/$defs/demultiplexing options" + }, + { + "$ref": "#/$defs/read modifications" + }, + { + "$ref": "#/$defs/filtering of processed reads" + }, + { + "$ref": "#/$defs/output parameters" + }, + { + "$ref": "#/$defs/debug" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index a692a39e..d2a17baf 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -320,9 +320,9 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -347,6 +347,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index 6685e64f..5a1d48ec 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3400,9 +3400,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3418,6 +3418,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/falco/nextflow_schema.json b/target/nextflow/falco/nextflow_schema.json index 35d4cfa6..d9520b4e 100644 --- a/target/nextflow/falco/nextflow_schema.json +++ b/target/nextflow/falco/nextflow_schema.json @@ -1,227 +1,149 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "falco", -"description": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data", -"type": "object", -"definitions": { - - - - "input arguments" : { - "title": "Input arguments", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files", - "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\";\"`. input fastq files" - - } - - -} -}, - - - "run arguments" : { - "title": "Run arguments", - "type": "object", - "description": "No description", - "properties": { - - - "nogroup": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp", - "help_text": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp. \nAll reports will show data for every base in \nthe read. WARNING: When using this option, \nyour plots may end up a ridiculous size. You \nhave been warned!\n" - , - "default":false - } - - - , - "contaminents": { - "type": - "string", - "description": "Type: `file`. Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against", - "help_text": "Type: `file`. Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against. The file \nmust contain sets of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n" - - } - - - , - "adapters": { - "type": - "string", - "description": "Type: `file`. Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library", - "help_text": "Type: `file`. Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library. The \nfile must contain sets of named adapters in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n" - - } - - - , - "limits": { - "type": - "string", - "description": "Type: `file`. Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules", - "help_text": "Type: `file`. Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules. This file can also be used \nto selectively remove some modules from the \noutput all together. The format needs to \nmirror the default limits.txt file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n" - - } - - - , - "subsample": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. [Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads)", - "help_text": "Type: `integer`, example: `10`. [Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n" - - } - - - , - "bisulfite": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content", - "help_text": "Type: `boolean_true`, default: `false`. [Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n" - , - "default":false - } - - - , - "reverse_complement": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [Falco only] The input is a \nreverse-complement", - "help_text": "Type: `boolean_true`, default: `false`. [Falco only] The input is a \nreverse-complement. All modules will be \ntested by swapping A/T and C/G\n" - , - "default":false - } - - -} -}, - - - "output arguments" : { - "title": "Output arguments", - "type": "object", - "description": "No description", - "properties": { - - - "outdir": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.outdir`, example: `output`. Create all output files in the specified \noutput directory", - "help_text": "Type: `file`, required, default: `$id.$key.outdir`, example: `output`. Create all output files in the specified \noutput directory. FALCO-SPECIFIC: If the \ndirectory does not exists, the program will \ncreate it.\n" - , - "default":"$id.$key.outdir" - } - - - , - "format": { - "type": - "string", - "description": "Type: `string`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format", - "help_text": "Type: `string`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped, sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n", - "enum": ["bam", "sam", "bam_mapped", "sam_mapped", "fastq", "fq", "fastq.gz", "fq.gz"] - - - } - - - , - "data_filename": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT)", - "help_text": "Type: `file`, default: `$id.$key.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT). If not specified, it will \nbe called fastq_data.txt in either the input \nfile\u0027s directory or the one specified in the \n--output flag. Only available when running \nfalco with a single input.\n" - , - "default":"$id.$key.data_filename" - } - - - , - "report_filename": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML)", - "help_text": "Type: `file`, default: `$id.$key.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" - , - "default":"$id.$key.report_filename" - } - - - , - "summary_filename": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT)", - "help_text": "Type: `file`, default: `$id.$key.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n" - , - "default":"$id.$key.summary_filename" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "falco", + "description": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data", + "type": "object", + "$defs": { + "input arguments": { + "title": "Input arguments", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "input fastq files", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input1.fastq;input2.fastq\"]`. " + } + } }, - - { - "$ref": "#/definitions/run arguments" + "run arguments": { + "title": "Run arguments", + "type": "object", + "description": "No description", + "properties": { + "nogroup": { + "type": "boolean", + "description": "Disable grouping of bases for reads >50bp", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "contaminents": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "adapters": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "limits": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "subsample": { + "type": "integer", + "description": "[Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "bisulfite": { + "type": "boolean", + "description": "[Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "reverse_complement": { + "type": "boolean", + "description": "[Falco only] The input is a \nreverse-complement", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/output arguments" + "output arguments": { + "title": "Output arguments", + "type": "object", + "description": "No description", + "properties": { + "outdir": { + "type": "string", + "format": "path", + "description": "Create all output files in the specified \noutput directory", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.outdir\"`, direction: `output`, example: `\"output\"`. ", + "default": "$id.$key.outdir" + }, + "format": { + "type": "string", + "description": "Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format", + "help_text": "Type: `string`, multiple: `False`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. ", + "enum": [ + "bam", + "sam", + "bam_mapped", + "sam_mapped", + "fastq", + "fq", + "fastq.gz", + "fq.gz" + ] + }, + "data_filename": { + "type": "string", + "format": "path", + "description": "[Falco only] Specify filename for FastQC \ndata output (TXT)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.data_filename\"`, direction: `output`. ", + "default": "$id.$key.data_filename" + }, + "report_filename": { + "type": "string", + "format": "path", + "description": "[Falco only] Specify filename for FastQC \nreport output (HTML)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.report_filename\"`, direction: `output`. ", + "default": "$id.$key.report_filename" + }, + "summary_filename": { + "type": "string", + "format": "path", + "description": "[Falco only] Specify filename for the short \nsummary output (TXT)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.summary_filename\"`, direction: `output`. ", + "default": "$id.$key.summary_filename" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input arguments" + }, + { + "$ref": "#/$defs/run arguments" + }, + { + "$ref": "#/$defs/output arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index 4db34ef5..e2f9e9ca 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1086,9 +1086,9 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1113,6 +1113,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index d2c279cc..a9a9ecdf 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -4253,9 +4253,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -4271,6 +4271,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fastp/nextflow_schema.json b/target/nextflow/fastp/nextflow_schema.json index 34670004..19a4640a 100644 --- a/target/nextflow/fastp/nextflow_schema.json +++ b/target/nextflow/fastp/nextflow_schema.json @@ -1,1131 +1,667 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "fastp", -"description": "An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n - filter out bad reads (too low quality, too short, or too many N...)\n - cut low quality bases for per read in its 5\u0027 and 3\u0027 by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n - trim all reads in front and tail\n - cut adapters. Adapter sequences can be automatically detected, which means you don\u0027t have to input the adapter sequences to trim them.\n - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n - trim polyG in 3\u0027 ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\u0027 ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n - report JSON format result for further interpreting.\n - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n - support long reads (data from PacBio / Nanopore devices).\n - support reading from STDIN and writing to STDOUT\n - support interleaved input\n - support ultra-fast FASTQ-level deduplication\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "`fastp` supports both single-end (SE) and paired-end (PE) input.\n\n- for SE data, you only have to specify read1 input by `-i` or `--in1`.\n- for PE data, you should also specify read2 input by `-I` or `--in2`.\n", - "properties": { - - - "in1": { - "type": - "string", - "description": "Type: `file`, required, example: `in.R1.fq.gz`. Input FastQ file", - "help_text": "Type: `file`, required, example: `in.R1.fq.gz`. Input FastQ file. Must be single-end or paired-end R1. Can be gzipped." - - } - - - , - "in2": { - "type": - "string", - "description": "Type: `file`, example: `in.R2.fq.gz`. Input FastQ file", - "help_text": "Type: `file`, example: `in.R2.fq.gz`. Input FastQ file. Must be paired-end R2. Can be gzipped." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "\n- for SE data, you only have to specify read1 output by `-o` or `--out1`.\n- for PE data, you should also specify read2 output by `-O` or `--out2`.\n- if you don\u0027t specify the output file names, no output files will be written, but the QC will still be done for both data before and after filtering.\n- the output will be gzip-compressed if its file name ends with `.gz`\n", - "properties": { - - - "out1": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC", - "help_text": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC. Will be gzipped if its file name ends with `.gz`." - , - "default":"$id.$key.out1.gz" - } - - - , - "out2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC", - "help_text": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC. Will be gzipped if its file name ends with `.gz`." - , - "default":"$id.$key.out2.gz" - } - - - , - "unpaired1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t", - "help_text": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t." - , - "default":"$id.$key.unpaired1.gz" - } - - - , - "unpaired2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t", - "help_text": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t." - , - "default":"$id.$key.unpaired2.gz" - } - - - , - "failed_out": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters", - "help_text": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters.\n\nIf one read failed and is written to --failed_out, its failure reason will be appended to its read name. For example, failed_quality_filter, failed_too_short etc.\nFor PE data, if unpaired reads are not stored (by giving --unpaired1 or --unpaired2), the failed pair of reads will be put together. If one read passes the filters but its pair doesn\u0027t, the failure reason will be paired_read_is_failing.\n" - , - "default":"$id.$key.failed_out.gz" - } - - - , - "overlapped_out": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base", - "help_text": "Type: `file`, default: `$id.$key.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n" - , - "default":"$id.$key.overlapped_out" - } - - -} -}, - - - "report output arguments" : { - "title": "Report output arguments", - "type": "object", - "description": "No description", - "properties": { - - - "json": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n", - "help_text": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n" - , - "default":"$id.$key.json.json" - } - - - , - "html": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n", - "help_text": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n" - , - "default":"$id.$key.html.html" - } - - - , - "report_title": { - "type": - "string", - "description": "Type: `string`, example: `fastp report`. The title of the html report, default is \"fastp report\"", - "help_text": "Type: `string`, example: `fastp report`. The title of the html report, default is \"fastp report\".\n" - - } - - -} -}, - - - "adapter trimming" : { - "title": "Adapter trimming", - "type": "object", - "description": "Adapter trimming is enabled by default, but you can disable it by `-A` or `--disable_adapter_trimming`. Adapter sequences can be automatically detected for both PE/SE data.\n\n- For SE data, the adapters are evaluated by analyzing the tails of first ~1M reads. This evaluation may be inacurrate, and you can specify the adapter sequence by `-a` or `--adapter_sequence` option. If adapter sequence is specified, the auto detection for SE data will be disabled.\n- For PE data, the adapters can be detected by per-read overlap analysis, which seeks for the overlap of each pair of reads. This method is robust and fast, so normally you don\u0027t have to input the adapter sequence even you know it. But you can still specify the adapter sequences for read1 by `--adapter_sequence`, and for read2 by `--adapter_sequence_r2`. If `fastp` fails to find an overlap (i.e. due to low quality bases), it will use these sequences to trim adapters for read1 and read2 respectively.\n- For PE data, the adapter sequence auto-detection is disabled by default since the adapters can be trimmed by overlap analysis. However, you can specify `--detect_adapter_for_pe` to enable it.\n- For PE data, `fastp` will run a little slower if you specify the sequence adapters or enable adapter auto-detection, but usually result in a slightly cleaner output, since the overlap analysis may fail due to sequencing errors or adapter dimers.\n- The most widely used adapter is the Illumina TruSeq adapters. If your data is from the TruSeq library, you can add `--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT` to your command lines, or enable auto detection for PE data by specifing `detect_adapter_for_pe`.\n- `fastp` contains some built-in known adapter sequences for better auto-detection. If you want to make some adapters to be a part of the built-in adapters, please file an issue.\n\nYou can also specify --adapter_fasta to give a FASTA file to tell fastp to trim multiple adapters in this FASTA file. Here is a sample of such adapter FASTA file:\n\n```\n\u003eIllumina TruSeq Adapter Read 1\nAGATCGGAAGAGCACACGTCTGAACTCCAGTCA\n\u003eIllumina TruSeq Adapter Read 2\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\n\u003epolyA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n```\n\nThe adapter sequence in this file should be at least 6bp long, otherwise it will be skipped. And you can give whatever you want to trim, rather than regular sequencing adapters (i.e. polyA).\n\n`fastp` first trims the auto-detected adapter or the adapter sequences given by `--adapter_sequence | --adapter_sequence_r2`, then trims the adapters given by `--adapter_fasta` one by one.\n\nThe sequence distribution of trimmed adapters can be found at the HTML/JSON reports.\n", - "properties": { - - - "disable_adapter_trimming": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable adapter trimming", - "help_text": "Type: `boolean_true`, default: `false`. Disable adapter trimming.\n" - , - "default":false - } - - - , - "detect_adapter_for_pe": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data", - "help_text": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.\n" - , - "default":false - } - - - , - "adapter_sequence": { - "type": - "string", - "description": "Type: `string`. The adapter sequences to be trimmed", - "help_text": "Type: `string`. The adapter sequences to be trimmed. For SE data, if not specified, the adapters will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped\n" - - } - - - , - "adapter_sequence_r2": { - "type": - "string", - "description": "Type: `string`. The adapter sequences to be trimmed for R2", - "help_text": "Type: `string`. The adapter sequences to be trimmed for R2. This is used for PE data if R1/R2 are found overlapped.\n" - - } - - - , - "adapter_fasta": { - "type": - "string", - "description": "Type: `file`. A FASTA file containing all the adapter sequences to be trimmed", - "help_text": "Type: `file`. A FASTA file containing all the adapter sequences to be trimmed. For SE data, if not specified, the adapters will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped.\n" - - } - - -} -}, - - - "base trimming" : { - "title": "Base trimming", - "type": "object", - "description": "No description", - "properties": { - - - "trim_front1": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Trimming how many bases in front for read1, default is 0", - "help_text": "Type: `integer`, example: `0`. Trimming how many bases in front for read1, default is 0.\n" - - } - - - , - "trim_tail1": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Trimming how many bases in tail for read1, default is 0", - "help_text": "Type: `integer`, example: `0`. Trimming how many bases in tail for read1, default is 0.\n" - - } - - - , - "max_len1": { - "type": - "integer", - "description": "Type: `integer`. If read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1", - "help_text": "Type: `integer`. If read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1. Default 0 means no limitation.\n" - - } - - - , - "trim_front2": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Trimming how many bases in front for read2, default is 0", - "help_text": "Type: `integer`, example: `0`. Trimming how many bases in front for read2, default is 0.\n" - - } - - - , - "trim_tail2": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Trimming how many bases in tail for read2, default is 0", - "help_text": "Type: `integer`, example: `0`. Trimming how many bases in tail for read2, default is 0.\n" - - } - - - , - "max_len2": { - "type": - "integer", - "description": "Type: `integer`. If read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2", - "help_text": "Type: `integer`. If read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2. Default 0 means no limitation.\n" - - } - - -} -}, - - - "merging mode" : { - "title": "Merging mode", - "type": "object", - "description": "Allows merging paired-end reads into a single longer read if they are overlapping.", - "properties": { - - - "merge": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped", - "help_text": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.\n" - , - "default":false - } - - - , - "merged_out": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output", - "help_text": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output.\n" - , - "default":"$id.$key.merged_out.gz" - } - - - , - "include_unmerged": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge", - "help_text": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.\n" - , - "default":false - } - - -} -}, - - - "additional input arguments" : { - "title": "Additional input arguments", - "type": "object", - "description": "Affects how the input is read.", - "properties": { - - - "interleaved_in": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2", - "help_text": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2. Disabled by default.\n" - , - "default":false - } - - - , - "fix_mgi_id": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it", - "help_text": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.\n" - , - "default":false - } - - - , - "phred64": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n", - "help_text": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n" - , - "default":false - } - - -} -}, - - - "additional output arguments" : { - "title": "Additional output arguments", - "type": "object", - "description": "Affects how the output is written.", - "properties": { - - - "compression": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. Compression level for gzip output (1 ~ 9)", - "help_text": "Type: `integer`, example: `4`. Compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 4.\n" - - } - - - , - "dont_overwrite": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files. Overwritting is allowed by default.\n" - , - "default":false - } - - -} -}, - - - "logging arguments" : { - "title": "Logging arguments", - "type": "object", - "description": "No description", - "properties": { - - - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output verbose log information (i", - "help_text": "Type: `boolean_true`, default: `false`. Output verbose log information (i.e. when every 1M reads are processed)." - , - "default":false - } - - -} -}, - - - "processing arguments" : { - "title": "Processing arguments", - "type": "object", - "description": "No description", - "properties": { - - - "reads_to_process": { - "type": - "string", - "description": "Type: `long`, example: `1000000`. Specify how many reads/pairs to be processed", - "help_text": "Type: `long`, example: `1000000`. Specify how many reads/pairs to be processed. Default 0 means process all reads.\n" - - } - - -} -}, - - - "deduplication arguments" : { - "title": "Deduplication arguments", - "type": "object", - "description": "No description", - "properties": { - - - "dedup": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n", - "help_text": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n" - , - "default":false - } - - - , - "dup_calc_accuracy": { - "type": - "integer", - "description": "Type: `integer`, example: `3`. Accuracy level to calculate duplication (1~6)", - "help_text": "Type: `integer`, example: `3`. Accuracy level to calculate duplication (1~6). Higher level uses more memory (1G, 2G, 4G, 8G, 16G, 24G). Default 1 for no-dedup mode, and 3 for dedup mode.\n" - - } - - - , - "dont_eval_duplication": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory.\n" - , - "default":false - } - - -} -}, - - - "polyg tail trimming arguments" : { - "title": "PolyG tail trimming arguments", - "type": "object", - "description": "No description", - "properties": { - - - "trim_poly_g": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", - "help_text": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n" - , - "default":false - } - - - , - "poly_g_min_len": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. The minimum length to detect polyG in the read tail", - "help_text": "Type: `integer`, example: `10`. The minimum length to detect polyG in the read tail. 10 by default.\n" - - } - - - , - "disable_trim_poly_g": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", - "help_text": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n" - , - "default":false - } - - -} -}, - - - "polyx tail trimming arguments" : { - "title": "PolyX tail trimming arguments", - "type": "object", - "description": "No description", - "properties": { - - - "trim_poly_x": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends", - "help_text": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends.\n" - , - "default":false - } - - - , - "poly_x_min_len": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. The minimum length to detect polyX in the read tail", - "help_text": "Type: `integer`, example: `10`. The minimum length to detect polyX in the read tail. 10 by default.\n" - - } - - -} -}, - - - "cut arguments" : { - "title": "Cut arguments", - "type": "object", - "description": "No description", - "properties": { - - - "cut_front": { - "type": - "integer", - "description": "Type: `integer`. Move a sliding window from front (5\u0027) to tail, drop the bases in the window if its mean quality \u003c threshold, stop otherwise", - "help_text": "Type: `integer`. Move a sliding window from front (5\u0027) to tail, drop the bases in the window if its mean quality \u003c threshold, stop otherwise.\n" - - } - - - , - "cut_tail": { - "type": - "integer", - "description": "Type: `integer`. Move a sliding window from tail (3\u0027) to front, drop the bases in the window if its mean quality \u003c threshold, stop otherwise", - "help_text": "Type: `integer`. Move a sliding window from tail (3\u0027) to front, drop the bases in the window if its mean quality \u003c threshold, stop otherwise.\n" - - } - - - , - "cut_right": { - "type": - "integer", - "description": "Type: `integer`. Move a sliding window from front to tail, if meet one window with mean quality \u003c threshold, drop the bases in the window and the right part, and then stop", - "help_text": "Type: `integer`. Move a sliding window from front to tail, if meet one window with mean quality \u003c threshold, drop the bases in the window and the right part, and then stop.\n" - - } - - - , - "cut_window_size": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. The window size option shared by cut_front, cut_tail or cut_sliding", - "help_text": "Type: `integer`, example: `4`. The window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4.\n" - - } - - - , - "cut_mean_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. The mean quality requirement option shared by cut_front, cut_tail or cut_sliding", - "help_text": "Type: `integer`, example: `20`. The mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20)\n" - - } - - - , - "cut_front_window_size": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. The window size option of cut_front, default to cut_window_size if not specified", - "help_text": "Type: `integer`, example: `4`. The window size option of cut_front, default to cut_window_size if not specified.\n" - - } - - - , - "cut_front_mean_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. The mean quality requirement option of cut_front, default to cut_mean_quality if not specified", - "help_text": "Type: `integer`, example: `20`. The mean quality requirement option of cut_front, default to cut_mean_quality if not specified.\n" - - } - - - , - "cut_tail_window_size": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. The window size option of cut_tail, default to cut_window_size if not specified", - "help_text": "Type: `integer`, example: `4`. The window size option of cut_tail, default to cut_window_size if not specified.\n" - - } - - - , - "cut_tail_mean_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. The mean quality requirement option of cut_tail, default to cut_mean_quality if not specified", - "help_text": "Type: `integer`, example: `20`. The mean quality requirement option of cut_tail, default to cut_mean_quality if not specified.\n" - - } - - - , - "cut_right_window_size": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. The window size option of cut_right, default to cut_window_size if not specified", - "help_text": "Type: `integer`, example: `4`. The window size option of cut_right, default to cut_window_size if not specified.\n" - - } - - - , - "cut_right_mean_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. The mean quality requirement option of cut_right, default to cut_mean_quality if not specified", - "help_text": "Type: `integer`, example: `20`. The mean quality requirement option of cut_right, default to cut_mean_quality if not specified.\n" - - } - - -} -}, - - - "quality filtering arguments" : { - "title": "Quality filtering arguments", - "type": "object", - "description": "No description", - "properties": { - - - "disable_quality_filtering": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default", - "help_text": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default. If this option is specified, quality filtering is disabled.\n" - , - "default":false - } - - - , - "qualified_quality_phred": { - "type": - "integer", - "description": "Type: `integer`, example: `15`. The quality value that a base is qualified", - "help_text": "Type: `integer`, example: `15`. The quality value that a base is qualified. Default 15 means phred quality \u003e=Q15 is qualified.\n" - - } - - - , - "unqualified_percent_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `40`. How many percents of bases are allowed to be unqualified (0~100)", - "help_text": "Type: `integer`, example: `40`. How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%.\n" - - } - - - , - "n_base_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. If one read\u0027s number of N base is \u003en_base_limit, then this read/pair is discarded", - "help_text": "Type: `integer`, example: `5`. If one read\u0027s number of N base is \u003en_base_limit, then this read/pair is discarded. Default is 5.\n" - - } - - - , - "average_qual": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. If one read\u0027s average quality score \u003cavg_qual, then this read/pair is discarded", - "help_text": "Type: `integer`, example: `0`. If one read\u0027s average quality score \u003cavg_qual, then this read/pair is discarded. Default 0 means no requirement.\n" - - } - - -} -}, - - - "length filtering arguments" : { - "title": "Length filtering arguments", - "type": "object", - "description": "No description", - "properties": { - - - "disable_length_filtering": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default", - "help_text": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default. If this option is specified, length filtering is disabled.\n" - , - "default":false - } - - - , - "length_required": { - "type": - "integer", - "description": "Type: `integer`, example: `15`. Reads shorter than length_required will be discarded, default is 15", - "help_text": "Type: `integer`, example: `15`. Reads shorter than length_required will be discarded, default is 15.\n" - - } - - - , - "length_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Reads longer than length_limit will be discarded, default 0 means no limitation", - "help_text": "Type: `integer`, example: `0`. Reads longer than length_limit will be discarded, default 0 means no limitation.\n" - - } - - -} -}, - - - "low complexity filtering arguments" : { - "title": "Low complexity filtering arguments", - "type": "object", - "description": "No description", - "properties": { - - - "low_complexity_filter": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable low complexity filter", - "help_text": "Type: `boolean_true`, default: `false`. Enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).\n" - , - "default":false - } - - - , - "complexity_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. The threshold for low complexity filter (0~100)", - "help_text": "Type: `integer`, example: `30`. The threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required.\n" - - } - - -} -}, - - - "index filtering arguments" : { - "title": "Index filtering arguments", - "type": "object", - "description": "No description", - "properties": { - - - "filter_by_index1": { - "type": - "string", - "description": "Type: `file`. Specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line", - "help_text": "Type: `file`. Specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line.\n" - - } - - - , - "filter_by_index2": { - "type": - "string", - "description": "Type: `file`. Specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line", - "help_text": "Type: `file`. Specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line.\n" - - } - - - , - "filter_by_index_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. The allowed difference of index barcode for index filtering, default 0 means completely identical", - "help_text": "Type: `integer`, example: `0`. The allowed difference of index barcode for index filtering, default 0 means completely identical.\n" - - } - - -} -}, - - - "overlapped region correction" : { - "title": "Overlapped region correction", - "type": "object", - "description": "No description", - "properties": { - - - "correction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled", - "help_text": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled.\n" - , - "default":false - } - - - , - "overlap_len_require": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. The minimum length to detect overlapped region of PE reads", - "help_text": "Type: `integer`, example: `30`. The minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default.\n" - - } - - - , - "overlap_diff_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. The maximum number of mismatched bases to detect overlapped region of PE reads", - "help_text": "Type: `integer`, example: `5`. The maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default.\n" - - } - - - , - "overlap_diff_percent_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. The maximum percentage of mismatched bases to detect overlapped region of PE reads", - "help_text": "Type: `integer`, example: `20`. The maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%.\n" - - } - - -} -}, - - - "umi arguments" : { - "title": "UMI arguments", - "type": "object", - "description": "No description", - "properties": { - - - "umi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing", - "help_text": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing.\n" - , - "default":false - } - - - , - "umi_loc": { - "type": - "string", - "description": "Type: `string`, choices: ``index1`, `index2`, `read1`, `read2`, `per_index`, `per_read``. Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none", - "help_text": "Type: `string`, choices: ``index1`, `index2`, `read1`, `read2`, `per_index`, `per_read``. Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none.\n", - "enum": ["index1", "index2", "read1", "read2", "per_index", "per_read"] - - - } - - - , - "umi_len": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. If the UMI is in read1/read2, its length should be provided", - "help_text": "Type: `integer`, example: `0`. If the UMI is in read1/read2, its length should be provided.\n" - - } - - - , - "umi_prefix": { - "type": - "string", - "description": "Type: `string`. If specified, an underline will be used to connect prefix and UMI (i", - "help_text": "Type: `string`. If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default.\n" - - } - - - , - "umi_skip": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. If the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0", - "help_text": "Type: `integer`, example: `0`. If the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0.\n" - - } - - - , - "umi_delim": { - "type": - "string", - "description": "Type: `string`. If the UMI is in index1/index2, fastp can use a delimiter to separate UMI from the read sequence, default is none", - "help_text": "Type: `string`. If the UMI is in index1/index2, fastp can use a delimiter to separate UMI from the read sequence, default is none.\n" - - } - - -} -}, - - - "overrepresentation analysis arguments" : { - "title": "Overrepresentation analysis arguments", - "type": "object", - "description": "No description", - "properties": { - - - "overrepresentation_analysis": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis", - "help_text": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis.\n" - , - "default":false - } - - - , - "overrepresentation_sampling": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20", - "help_text": "Type: `integer`, example: `20`. One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "fastp", + "description": "An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n - filter out bad reads (too low quality, too short, or too many N...)\n - cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n - trim all reads in front and tail\n - cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.\n - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n - trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n - report JSON format result for further interpreting.\n - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n - support long reads (data from PacBio / Nanopore devices).\n - support reading from STDIN and writing to STDOUT\n - support interleaved input\n - support ultra-fast FASTQ-level deduplication\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "`fastp` supports both single-end (SE) and paired-end (PE) input.\n\n- for SE data, you only have to specify read1 input by `-i` or `--in1`.\n- for PE data, you should also specify read2 input by `-I` or `--in2`.\n", + "properties": { + "in1": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input FastQ file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"in.R1.fq.gz\"`. " + }, + "in2": { + "type": "string", + "format": "path", + "description": "Input FastQ file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"in.R2.fq.gz\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "\n- for SE data, you only have to specify read1 output by `-o` or `--out1`.\n- for PE data, you should also specify read2 output by `-O` or `--out2`.\n- if you don't specify the output file names, no output files will be written, but the QC will still be done for both data before and after filtering.\n- the output will be gzip-compressed if its file name ends with `.gz`\n", + "properties": { + "out1": { + "type": "string", + "format": "path", + "description": "The single-end or paired-end R1 reads that pass QC", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.out1.gz\"`, direction: `output`, example: `\"out.R1.fq.gz\"`. ", + "default": "$id.$key.out1.gz" + }, + "out2": { + "type": "string", + "format": "path", + "description": "The paired-end R2 reads that pass QC", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.out2.gz\"`, direction: `output`, example: `\"out.R2.fq.gz\"`. ", + "default": "$id.$key.out2.gz" + }, + "unpaired1": { + "type": "string", + "format": "path", + "description": "Store the reads that `read1` passes filters but its paired `read2` doesn't.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unpaired1.gz\"`, direction: `output`, example: `\"unpaired.R1.fq.gz\"`. ", + "default": "$id.$key.unpaired1.gz" + }, + "unpaired2": { + "type": "string", + "format": "path", + "description": "Store the reads that `read2` passes filters but its paired `read1` doesn't.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unpaired2.gz\"`, direction: `output`, example: `\"unpaired.R2.fq.gz\"`. ", + "default": "$id.$key.unpaired2.gz" + }, + "failed_out": { + "type": "string", + "format": "path", + "description": "Store the reads that fail filters.\n\nIf one read failed and is written to --failed_out, its failure reason will be appended to its read name", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.failed_out.gz\"`, direction: `output`, example: `\"failed.fq.gz\"`. ", + "default": "$id.$key.failed_out.gz" + }, + "overlapped_out": { + "type": "string", + "format": "path", + "description": "For each read pair, output the overlapped region if it has no any mismatched base.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.overlapped_out\"`, direction: `output`. ", + "default": "$id.$key.overlapped_out" + } + } }, - - { - "$ref": "#/definitions/report output arguments" + "report output arguments": { + "title": "Report output arguments", + "type": "object", + "description": "No description", + "properties": { + "json": { + "type": "string", + "format": "path", + "description": "The json format report file name\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.json.json\"`, direction: `output`, example: `\"out.json\"`. ", + "default": "$id.$key.json.json" + }, + "html": { + "type": "string", + "format": "path", + "description": "The html format report file name\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.html.html\"`, direction: `output`, example: `\"out.html\"`. ", + "default": "$id.$key.html.html" + }, + "report_title": { + "type": "string", + "description": "The title of the html report, default is \"fastp report\".\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"fastp report\"`. " + } + } }, - - { - "$ref": "#/definitions/adapter trimming" + "adapter trimming": { + "title": "Adapter trimming", + "type": "object", + "description": "Adapter trimming is enabled by default, but you can disable it by `-A` or `--disable_adapter_trimming`. Adapter sequences can be automatically detected for both PE/SE data.\n\n- For SE data, the adapters are evaluated by analyzing the tails of first ~1M reads. This evaluation may be inacurrate, and you can specify the adapter sequence by `-a` or `--adapter_sequence` option. If adapter sequence is specified, the auto detection for SE data will be disabled.\n- For PE data, the adapters can be detected by per-read overlap analysis, which seeks for the overlap of each pair of reads. This method is robust and fast, so normally you don't have to input the adapter sequence even you know it. But you can still specify the adapter sequences for read1 by `--adapter_sequence`, and for read2 by `--adapter_sequence_r2`. If `fastp` fails to find an overlap (i.e. due to low quality bases), it will use these sequences to trim adapters for read1 and read2 respectively.\n- For PE data, the adapter sequence auto-detection is disabled by default since the adapters can be trimmed by overlap analysis. However, you can specify `--detect_adapter_for_pe` to enable it.\n- For PE data, `fastp` will run a little slower if you specify the sequence adapters or enable adapter auto-detection, but usually result in a slightly cleaner output, since the overlap analysis may fail due to sequencing errors or adapter dimers.\n- The most widely used adapter is the Illumina TruSeq adapters. If your data is from the TruSeq library, you can add `--adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT` to your command lines, or enable auto detection for PE data by specifing `detect_adapter_for_pe`.\n- `fastp` contains some built-in known adapter sequences for better auto-detection. If you want to make some adapters to be a part of the built-in adapters, please file an issue.\n\nYou can also specify --adapter_fasta to give a FASTA file to tell fastp to trim multiple adapters in this FASTA file. Here is a sample of such adapter FASTA file:\n\n```\n>Illumina TruSeq Adapter Read 1\nAGATCGGAAGAGCACACGTCTGAACTCCAGTCA\n>Illumina TruSeq Adapter Read 2\nAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\n>polyA\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n```\n\nThe adapter sequence in this file should be at least 6bp long, otherwise it will be skipped. And you can give whatever you want to trim, rather than regular sequencing adapters (i.e. polyA).\n\n`fastp` first trims the auto-detected adapter or the adapter sequences given by `--adapter_sequence | --adapter_sequence_r2`, then trims the adapters given by `--adapter_fasta` one by one.\n\nThe sequence distribution of trimmed adapters can be found at the HTML/JSON reports.\n", + "properties": { + "disable_adapter_trimming": { + "type": "boolean", + "description": "Disable adapter trimming.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "detect_adapter_for_pe": { + "type": "boolean", + "description": "By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "adapter_sequence": { + "type": "string", + "description": "The adapter sequences to be trimmed", + "help_text": "Type: `string`, multiple: `False`. " + }, + "adapter_sequence_r2": { + "type": "string", + "description": "The adapter sequences to be trimmed for R2", + "help_text": "Type: `string`, multiple: `False`. " + }, + "adapter_fasta": { + "type": "string", + "format": "path", + "description": "A FASTA file containing all the adapter sequences to be trimmed", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/base trimming" + "base trimming": { + "title": "Base trimming", + "type": "object", + "description": "No description", + "properties": { + "trim_front1": { + "type": "integer", + "description": "Trimming how many bases in front for read1, default is 0.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "trim_tail1": { + "type": "integer", + "description": "Trimming how many bases in tail for read1, default is 0.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "max_len1": { + "type": "integer", + "description": "If read1 is longer than max_len1, then trim read1 at its tail to make it as long as max_len1", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "trim_front2": { + "type": "integer", + "description": "Trimming how many bases in front for read2, default is 0.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "trim_tail2": { + "type": "integer", + "description": "Trimming how many bases in tail for read2, default is 0.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "max_len2": { + "type": "integer", + "description": "If read2 is longer than max_len2, then trim read2 at its tail to make it as long as max_len2", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/merging mode" + "merging mode": { + "title": "Merging mode", + "type": "object", + "description": "Allows merging paired-end reads into a single longer read if they are overlapping.", + "properties": { + "merge": { + "type": "boolean", + "description": "For paired-end input, merge each pair of reads into a single read if they are overlapped", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "merged_out": { + "type": "string", + "format": "path", + "description": "In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.merged_out.gz\"`, direction: `output`, example: `\"merged.fq.gz\"`. ", + "default": "$id.$key.merged_out.gz" + }, + "include_unmerged": { + "type": "boolean", + "description": "In the merging mode, write the unmerged or unpaired reads to the file specified by --merge", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/additional input arguments" + "additional input arguments": { + "title": "Additional input arguments", + "type": "object", + "description": "Affects how the input is read.", + "properties": { + "interleaved_in": { + "type": "boolean", + "description": "Indicate that is an interleaved FASTQ which contains both read1 and read2", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fix_mgi_id": { + "type": "boolean", + "description": "The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "phred64": { + "type": "boolean", + "description": "Indicate the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/additional output arguments" + "additional output arguments": { + "title": "Additional output arguments", + "type": "object", + "description": "Affects how the output is written.", + "properties": { + "compression": { + "type": "integer", + "description": "Compression level for gzip output (1 ~ 9)", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "dont_overwrite": { + "type": "boolean", + "description": "Don't overwrite existing files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/logging arguments" + "logging arguments": { + "title": "Logging arguments", + "type": "object", + "description": "No description", + "properties": { + "verbose": { + "type": "boolean", + "description": "Output verbose log information (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/processing arguments" + "processing arguments": { + "title": "Processing arguments", + "type": "object", + "description": "No description", + "properties": { + "reads_to_process": { + "type": "string", + "description": "Specify how many reads/pairs to be processed", + "help_text": "Type: `long`, multiple: `False`, example: `1000000`. " + } + } }, - - { - "$ref": "#/definitions/deduplication arguments" + "deduplication arguments": { + "title": "Deduplication arguments", + "type": "object", + "description": "No description", + "properties": { + "dedup": { + "type": "boolean", + "description": "Enable deduplication to drop the duplicated reads/pairs\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dup_calc_accuracy": { + "type": "integer", + "description": "Accuracy level to calculate duplication (1~6)", + "help_text": "Type: `integer`, multiple: `False`, example: `3`. " + }, + "dont_eval_duplication": { + "type": "boolean", + "description": "Don't evaluate duplication rate to save time and use less memory.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/polyg tail trimming arguments" + "polyg tail trimming arguments": { + "title": "PolyG tail trimming arguments", + "type": "object", + "description": "No description", + "properties": { + "trim_poly_g": { + "type": "boolean", + "description": "Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "poly_g_min_len": { + "type": "integer", + "description": "The minimum length to detect polyG in the read tail", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "disable_trim_poly_g": { + "type": "boolean", + "description": "Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/polyx tail trimming arguments" + "polyx tail trimming arguments": { + "title": "PolyX tail trimming arguments", + "type": "object", + "description": "No description", + "properties": { + "trim_poly_x": { + "type": "boolean", + "description": "Enable polyX trimming in 3' ends.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "poly_x_min_len": { + "type": "integer", + "description": "The minimum length to detect polyX in the read tail", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + } + } }, - - { - "$ref": "#/definitions/cut arguments" + "cut arguments": { + "title": "Cut arguments", + "type": "object", + "description": "No description", + "properties": { + "cut_front": { + "type": "integer", + "description": "Move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "cut_tail": { + "type": "integer", + "description": "Move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "cut_right": { + "type": "integer", + "description": "Move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "cut_window_size": { + "type": "integer", + "description": "The window size option shared by cut_front, cut_tail or cut_sliding", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "cut_mean_quality": { + "type": "integer", + "description": "The mean quality requirement option shared by cut_front, cut_tail or cut_sliding", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "cut_front_window_size": { + "type": "integer", + "description": "The window size option of cut_front, default to cut_window_size if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "cut_front_mean_quality": { + "type": "integer", + "description": "The mean quality requirement option of cut_front, default to cut_mean_quality if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "cut_tail_window_size": { + "type": "integer", + "description": "The window size option of cut_tail, default to cut_window_size if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "cut_tail_mean_quality": { + "type": "integer", + "description": "The mean quality requirement option of cut_tail, default to cut_mean_quality if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "cut_right_window_size": { + "type": "integer", + "description": "The window size option of cut_right, default to cut_window_size if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "cut_right_mean_quality": { + "type": "integer", + "description": "The mean quality requirement option of cut_right, default to cut_mean_quality if not specified.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + } + } }, - - { - "$ref": "#/definitions/quality filtering arguments" + "quality filtering arguments": { + "title": "Quality filtering arguments", + "type": "object", + "description": "No description", + "properties": { + "disable_quality_filtering": { + "type": "boolean", + "description": "Quality filtering is enabled by default", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "qualified_quality_phred": { + "type": "integer", + "description": "The quality value that a base is qualified", + "help_text": "Type: `integer`, multiple: `False`, example: `15`. " + }, + "unqualified_percent_limit": { + "type": "integer", + "description": "How many percents of bases are allowed to be unqualified (0~100)", + "help_text": "Type: `integer`, multiple: `False`, example: `40`. " + }, + "n_base_limit": { + "type": "integer", + "description": "If one read's number of N base is >n_base_limit, then this read/pair is discarded", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "average_qual": { + "type": "integer", + "description": "If one read's average quality score 50bp", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_length": { + "type": "integer", + "description": "Sets an artificial lower limit on the length of the \nsequence to be shown in the report", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "format": { + "type": "string", + "description": "Bypasses the normal sequence file format detection and \nforces the program to use the specified format", + "help_text": "Type: `string`, multiple: `False`, example: `\"bam\"`. " + }, + "contaminants": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains the list \nof contaminants to screen overrepresented sequences against", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"contaminants.txt\"`. " + }, + "adapters": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains the list of \nadapter sequences which will be explicitly searched against \nthe library", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"adapters.txt\"`. " + }, + "limits": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains \na set of criteria which will be used to determine \nthe warn/error limits for the various modules", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"limits.txt\"`. " + }, + "kmers": { + "type": "integer", + "description": "Specifies the length of Kmer to look for in the Kmer \ncontent module", + "help_text": "Type: `integer`, multiple: `False`, example: `7`. " + }, + "quiet": { + "type": "boolean", + "description": "Suppress all progress messages on stdout and only report errors.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 32c1b74e..066d6f91 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -648,9 +643,9 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -675,6 +670,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 000b4d29..96fb7b94 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3044,17 +3044,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -3779,9 +3771,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3797,6 +3789,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/featurecounts/nextflow_schema.json b/target/nextflow/featurecounts/nextflow_schema.json index 9276bfa3..6f4e673e 100644 --- a/target/nextflow/featurecounts/nextflow_schema.json +++ b/target/nextflow/featurecounts/nextflow_schema.json @@ -1,726 +1,455 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "featurecounts", -"description": "featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "annotation": { - "type": - "string", - "description": "Type: `file`, required, example: `annotation.gtf`. Name of an annotation file", - "help_text": "Type: `file`, required, example: `annotation.gtf`. Name of an annotation file. GTF/GFF format by default. See \u0027--format\u0027 option for more format information.\n" - - } - - - , - "input": { - "type": - "string", - "description": "Type: List of `file`, required, example: `input_file1.bam`, multiple_sep: `\";\"`. A list of SAM or BAM format files separated by semi-colon (;)", - "help_text": "Type: List of `file`, required, example: `input_file1.bam`, multiple_sep: `\";\"`. A list of SAM or BAM format files separated by semi-colon (;). They can be either name or location sorted. Location-sorted paired-end reads are automatically sorted by read names.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "counts": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format", - "help_text": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format.\n" - , - "default":"$id.$key.counts.tsv" - } - - - , - "summary": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format", - "help_text": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format.\n" - , - "default":"$id.$key.summary.tsv" - } - - - , - "junctions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction", - "help_text": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction. Junctions were identified from those exon-spanning reads in the input (containing \u0027N\u0027 in CIGAR string).\n" - , - "default":"$id.$key.junctions.txt" - } - - -} -}, - - - "annotation" : { - "title": "Annotation", - "type": "object", - "description": "No description", - "properties": { - - - "format": { - "type": - "string", - "description": "Type: `string`, example: `GTF`, choices: ``GTF`, `GFF`, `SAF``. Specify format of the provided annotation file", - "help_text": "Type: `string`, example: `GTF`, choices: ``GTF`, `GFF`, `SAF``. Specify format of the provided annotation file. Acceptable formats include \u0027GTF\u0027 (or compatible GFF format) and \u0027SAF\u0027. \u0027GTF\u0027 by default. \n", - "enum": ["GTF", "GFF", "SAF"] - - - } - - - , - "feature_type": { - "type": - "string", - "description": "Type: List of `string`, example: `exon`, multiple_sep: `\";\"`. Specify feature type(s) in a GTF annotation", - "help_text": "Type: List of `string`, example: `exon`, multiple_sep: `\";\"`. Specify feature type(s) in a GTF annotation. If multiple types are provided, they should be separated by \u0027;\u0027 with no space in between. \u0027exon\u0027 by default. Rows in the annotation with a matched feature will be extracted and used for read mapping.\n" - - } - - - , - "attribute_type": { - "type": - "string", - "description": "Type: `string`, example: `gene_id`. Specify attribute type in GTF annotation", - "help_text": "Type: `string`, example: `gene_id`. Specify attribute type in GTF annotation. \u0027gene_id\u0027 by default. Meta-features used for read counting will be extracted from annotation using the provided value.\n" - - } - - - , - "extra_attributes": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Extract extra attribute types from the provided GTF annotation and include them in the counting output", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Extract extra attribute types from the provided GTF annotation and include them in the counting output. These attribute types will not be used to group features. If more than one attribute type is provided they should be separated by semicolon (;).\n" - - } - - - , - "chrom_alias": { - "type": - "string", - "description": "Type: `file`, example: `chrom_alias.csv`. Provide a chromosome name alias file to match chr names in annotation with those in the reads", - "help_text": "Type: `file`, example: `chrom_alias.csv`. Provide a chromosome name alias file to match chr names in annotation with those in the reads. This should be a two-column comma-delimited text file. Its first column should include chr names in the annotation and its second column should include chr names in the reads. Chr names are case sensitive. No column header should be included in the file.\n" - - } - - -} -}, - - - "level of summarization" : { - "title": "Level of summarization", - "type": "object", - "description": "No description", - "properties": { - - - "feature_level": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg", - "help_text": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg. counting reads for exons rather than genes).\n" - , - "default":false - } - - -} -}, - - - "overlap between reads and features" : { - "title": "Overlap between reads and features", - "type": "object", - "description": "No description", - "properties": { - - - "overlapping": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified)", - "help_text": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified).\n" - , - "default":false - } - - - , - "min_overlap": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Minimum number of overlapping bases in a read that is required for read assignment", - "help_text": "Type: `integer`, example: `1`. Minimum number of overlapping bases in a read that is required for read assignment. 1 by default. Number of overlapping bases is counted from both reads if paired end. If a negative value is provided, then a gap of up to specified size will be allowed between read and the feature that the read is assigned to.\n" - - } - - - , - "frac_overlap": { - "type": - "number", - "description": "Type: `double`, example: `0.0`. Minimum fraction of overlapping bases in a read that is required for read assignment", - "help_text": "Type: `double`, example: `0.0`. Minimum fraction of overlapping bases in a read that is required for read assignment. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and \u0027--min_overlap\u0027 option need to be satisfied for read assignment.\n" - - } - - - , - "frac_overlap_feature": { - "type": - "number", - "description": "Type: `double`, example: `0.0`. Minimum fraction of overlapping bases in a feature that is required for read assignment", - "help_text": "Type: `double`, example: `0.0`. Minimum fraction of overlapping bases in a feature that is required for read assignment. Value should be within range [0,1]. 0 by default.\n" - - } - - - , - "largest_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases", - "help_text": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases.\n" - , - "default":false - } - - - , - "non_overlap": { - "type": - "integer", - "description": "Type: `integer`. Maximum number of non-overlapping bases in a read (or a read pair) that is allowed when being assigned to a feature", - "help_text": "Type: `integer`. Maximum number of non-overlapping bases in a read (or a read pair) that is allowed when being assigned to a feature. No limit is set by default.\n" - - } - - - , - "non_overlap_feature": { - "type": - "integer", - "description": "Type: `integer`. Maximum number of non-overlapping bases in a feature that is allowed in read assignment", - "help_text": "Type: `integer`. Maximum number of non-overlapping bases in a feature that is allowed in read assignment. No limit is set by default.\n" - - } - - - , - "read_extension5": { - "type": - "integer", - "description": "Type: `integer`. Reads are extended upstream by \u003cint\u003e bases from their 5\u0027 end", - "help_text": "Type: `integer`. Reads are extended upstream by \u003cint\u003e bases from their 5\u0027 end.\n" - - } - - - , - "read_extension3": { - "type": - "integer", - "description": "Type: `integer`. Reads are extended upstream by \u003cint\u003e bases from their 3\u0027 end", - "help_text": "Type: `integer`. Reads are extended upstream by \u003cint\u003e bases from their 3\u0027 end.\n" - - } - - - , - "read2pos": { - "type": - "integer", - "description": "Type: `integer`, choices: ``3`, `5``. Reduce reads to their 5\u0027 most base or 3\u0027 most base", - "help_text": "Type: `integer`, choices: ``3`, `5``. Reduce reads to their 5\u0027 most base or 3\u0027 most base. Read counting is then performed based on the single base the read is reduced to.\n", - "enum": [3, 5] - - - } - - -} -}, - - - "multi-mapping reads" : { - "title": "Multi-mapping reads", - "type": "object", - "description": "No description", - "properties": { - - - "multi_mapping": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted", - "help_text": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted. For a multi-mapping read, all its reported alignments will be counted. The \u0027NH\u0027 tag in BAM/SAM input is used to detect multi-mapping reads.\n" - , - "default":false - } - - -} -}, - - - "fractional counting" : { - "title": "Fractional counting", - "type": "object", - "description": "No description", - "properties": { - - - "fraction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Assign fractional counts to features", - "help_text": "Type: `boolean_true`, default: `false`. Assign fractional counts to features. This option must be used together with \u0027--multi_mapping\u0027 or \u0027--overlapping\u0027 or both. When \u0027--multi_mapping\u0027 is specified, each reported alignment from a multi-mapping read (identified via \u0027NH\u0027 tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When \u0027--overlapping\u0027 is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both \u0027--multi_mapping\u0027 and \u0027--overlapping\u0027 are specified, each alignment will carry a fractional count of 1/(x*y).\n" - , - "default":false - } - - -} -}, - - - "read filtering" : { - "title": "Read filtering", - "type": "object", - "description": "No description", - "properties": { - - - "min_map_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. The minimum mapping quality score a read must satisfy in order to be counted", - "help_text": "Type: `integer`, example: `0`. The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default.\n" - - } - - - , - "split_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count split alignments only (ie", - "help_text": "Type: `boolean_true`, default: `false`. Count split alignments only (ie. alignments with CIGAR string containing \u0027N\u0027). An example of split alignments is exon-spanning reads in RNA-seq data.\n" - , - "default":false - } - - - , - "non_split_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted", - "help_text": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted. All the other alignments will be ignored.\n" - , - "default":false - } - - - , - "primary": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count primary alignments only", - "help_text": "Type: `boolean_true`, default: `false`. Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.\n" - , - "default":false - } - - - , - "ignore_dup": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting", - "help_text": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting. Duplicate reads are identified using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is a duplicate read for paired end data.\n" - , - "default":false - } - - -} -}, - - - "strandedness" : { - "title": "Strandedness", - "type": "object", - "description": "No description", - "properties": { - - - "strand": { - "type": - "integer", - "description": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. Perform strand-specific read counting", - "help_text": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. Perform strand-specific read counting. A single integer value (applied to all input files) should be provided. Possible values include: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). Default value is 0 (ie. unstranded read counting carried out for all input files).\n", - "enum": [0, 1, 2] - - - } - - -} -}, - - - "exon-exon junctions" : { - "title": "Exon-exon junctions", - "type": "object", - "description": "No description", - "properties": { - - - "ref_fasta": { - "type": - "string", - "description": "Type: `file`, example: `reference.fasta`. Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files", - "help_text": "Type: `file`, example: `reference.fasta`. Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files.\n" - - } - - -} -}, - - - "parameters specific to paired end reads" : { - "title": "Parameters specific to paired end reads", - "type": "object", - "description": "No description", - "properties": { - - - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads", - "help_text": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads. To perform fragment counting (ie. counting read pairs), the \u0027--countReadPairs\u0027 parameter should also be specified in addition to this parameter.\n" - , - "default":false - } - - - , - "count_read_pairs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads", - "help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n" - , - "default":false - } - - - , - "both_aligned": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads", - "help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n" - , - "default":false - } - - - , - "check_pe_dist": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs", - "help_text": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs. Use \u0027--min_length\u0027 and \u0027--max_length\u0027 to set thresholds.\n" - , - "default":false - } - - - , - "min_length": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. Minimum fragment/template length, 50 by default", - "help_text": "Type: `integer`, example: `50`. Minimum fragment/template length, 50 by default.\n" - - } - - - , - "max_length": { - "type": - "integer", - "description": "Type: `integer`, example: `600`. Maximum fragment/template length, 600 by default", - "help_text": "Type: `integer`, example: `600`. Maximum fragment/template length, 600 by default.\n" - - } - - - , - "same_strand": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands", - "help_text": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.\n" - , - "default":false - } - - - , - "donotsort": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input", - "help_text": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input. Note that reads from the same pair are required to be located next to each other in the input.\n" - , - "default":false - } - - -} -}, - - - "read groups" : { - "title": "Read groups", - "type": "object", - "description": "No description", - "properties": { - - - "by_read_group": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Assign reads by read group", - "help_text": "Type: `boolean_true`, default: `false`. Assign reads by read group. \"RG\" tag is required to be present in the input BAM/SAM files.\n" - , - "default":false - } - - -} -}, - - - "long reads" : { - "title": "Long reads", - "type": "object", - "description": "No description", - "properties": { - - - "long_reads": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads", - "help_text": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads. Long read counting can only run in one thread and only reads (not read-pairs) can be counted. There is no limitation on the number of \u0027M\u0027 operations allowed in a CIGAR string in long read counting.\n" - , - "default":false - } - - -} -}, - - - "assignment results for each read" : { - "title": "Assignment results for each read", - "type": "object", - "description": "No description", - "properties": { - - - "detailed_results": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results", - "help_text": "Type: `file`, default: `$id.$key.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n" - , - "default":"$id.$key.detailed_results" - } - - - , - "detailed_results_format": { - "type": - "string", - "description": "Type: `string`, choices: ``CORE`, `SAM`, `BAM``. Output detailed assignment results for each read or read-pair", - "help_text": "Type: `string`, choices: ``CORE`, `SAM`, `BAM``. Output detailed assignment results for each read or read-pair. Results are saved to a file that is in one of the following formats: CORE, SAM and BAM. See documentaiton for more info about these formats.\n", - "enum": ["CORE", "SAM", "BAM"] - - - } - - -} -}, - - - "miscellaneous" : { - "title": "Miscellaneous", - "type": "object", - "description": "No description", - "properties": { - - - "max_M_op": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. Maximum number of \u0027M\u0027 operations allowed in a CIGAR string", - "help_text": "Type: `integer`, example: `10`. Maximum number of \u0027M\u0027 operations allowed in a CIGAR string. 10 by default. Both \u0027X\u0027 and \u0027=\u0027 are treated as \u0027M\u0027 and adjacent \u0027M\u0027 operations are merged in the CIGAR string.\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names", - "help_text": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "featurecounts", + "description": "featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "annotation": { + "type": "string", + "format": "path", + "exists": true, + "description": "Name of an annotation file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"annotation.gtf\"`. " + }, + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "A list of SAM or BAM format files separated by semi-colon (;)", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input_file1.bam\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "counts": { + "type": "string", + "format": "path", + "description": "Name of output file including read counts in tab delimited format.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.counts.tsv\"`, direction: `output`, example: `\"features.tsv\"`. ", + "default": "$id.$key.counts.tsv" + }, + "summary": { + "type": "string", + "format": "path", + "description": "Summary statistics of counting results in tab delimited format.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.summary.tsv\"`, direction: `output`, example: `\"summary.tsv\"`. ", + "default": "$id.$key.summary.tsv" + }, + "junctions": { + "type": "string", + "format": "path", + "description": "Count number of reads supporting each exon-exon junction", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.junctions.txt\"`, direction: `output`, example: `\"junctions.txt\"`. ", + "default": "$id.$key.junctions.txt" + } + } }, - - { - "$ref": "#/definitions/annotation" + "annotation": { + "title": "Annotation", + "type": "object", + "description": "No description", + "properties": { + "format": { + "type": "string", + "description": "Specify format of the provided annotation file", + "help_text": "Type: `string`, multiple: `False`, example: `\"GTF\"`, choices: ``GTF`, `GFF`, `SAF``. ", + "enum": [ + "GTF", + "GFF", + "SAF" + ] + }, + "feature_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Specify feature type(s) in a GTF annotation", + "help_text": "Type: `string`, multiple: `True`, example: `[\"exon\"]`. " + }, + "attribute_type": { + "type": "string", + "description": "Specify attribute type in GTF annotation", + "help_text": "Type: `string`, multiple: `False`, example: `\"gene_id\"`. " + }, + "extra_attributes": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Extract extra attribute types from the provided GTF annotation and include them in the counting output", + "help_text": "Type: `string`, multiple: `True`. " + }, + "chrom_alias": { + "type": "string", + "format": "path", + "description": "Provide a chromosome name alias file to match chr names in annotation with those in the reads", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"chrom_alias.csv\"`. " + } + } }, - - { - "$ref": "#/definitions/level of summarization" + "level of summarization": { + "title": "Level of summarization", + "type": "object", + "description": "No description", + "properties": { + "feature_level": { + "type": "boolean", + "description": "Perform read counting at feature level (eg", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/overlap between reads and features" + "overlap between reads and features": { + "title": "Overlap between reads and features", + "type": "object", + "description": "No description", + "properties": { + "overlapping": { + "type": "boolean", + "description": "Assign reads to all their overlapping meta-features (or features if '--feature_level' is specified).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_overlap": { + "type": "integer", + "description": "Minimum number of overlapping bases in a read that is required for read assignment", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "frac_overlap": { + "type": "number", + "description": "Minimum fraction of overlapping bases in a read that is required for read assignment", + "help_text": "Type: `double`, multiple: `False`, example: `0.0`. " + }, + "frac_overlap_feature": { + "type": "number", + "description": "Minimum fraction of overlapping bases in a feature that is required for read assignment", + "help_text": "Type: `double`, multiple: `False`, example: `0.0`. " + }, + "largest_overlap": { + "type": "boolean", + "description": "Assign reads to a meta-feature/feature that has the largest number of overlapping bases.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "non_overlap": { + "type": "integer", + "description": "Maximum number of non-overlapping bases in a read (or a read pair) that is allowed when being assigned to a feature", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "non_overlap_feature": { + "type": "integer", + "description": "Maximum number of non-overlapping bases in a feature that is allowed in read assignment", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "read_extension5": { + "type": "integer", + "description": "Reads are extended upstream by bases from their 5' end.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "read_extension3": { + "type": "integer", + "description": "Reads are extended upstream by bases from their 3' end.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "read2pos": { + "type": "integer", + "description": "Reduce reads to their 5' most base or 3' most base", + "help_text": "Type: `integer`, multiple: `False`, choices: ``3`, `5``. ", + "enum": [ + 3, + 5 + ] + } + } }, - - { - "$ref": "#/definitions/multi-mapping reads" + "multi-mapping reads": { + "title": "Multi-mapping reads", + "type": "object", + "description": "No description", + "properties": { + "multi_mapping": { + "type": "boolean", + "description": "Multi-mapping reads will also be counted", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/fractional counting" + "fractional counting": { + "title": "Fractional counting", + "type": "object", + "description": "No description", + "properties": { + "fraction": { + "type": "boolean", + "description": "Assign fractional counts to features", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/read filtering" + "read filtering": { + "title": "Read filtering", + "type": "object", + "description": "No description", + "properties": { + "min_map_quality": { + "type": "integer", + "description": "The minimum mapping quality score a read must satisfy in order to be counted", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "split_only": { + "type": "boolean", + "description": "Count split alignments only (ie", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "non_split_only": { + "type": "boolean", + "description": "If specified, only non-split alignments (CIGAR strings do not contain letter 'N') will be counted", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "primary": { + "type": "boolean", + "description": "Count primary alignments only", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ignore_dup": { + "type": "boolean", + "description": "Ignore duplicate reads in read counting", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/strandedness" + "strandedness": { + "title": "Strandedness", + "type": "object", + "description": "No description", + "properties": { + "strand": { + "type": "integer", + "description": "Perform strand-specific read counting", + "help_text": "Type: `integer`, multiple: `False`, example: `0`, choices: ``0`, `1`, `2``. ", + "enum": [ + 0, + 1, + 2 + ] + } + } }, - - { - "$ref": "#/definitions/exon-exon junctions" + "exon-exon junctions": { + "title": "Exon-exon junctions", + "type": "object", + "description": "No description", + "properties": { + "ref_fasta": { + "type": "string", + "format": "path", + "description": "Provide the name of a FASTA-format file that contains the reference sequences used in read mapping that produced the provided SAM/BAM files.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reference.fasta\"`. " + } + } }, - - { - "$ref": "#/definitions/parameters specific to paired end reads" + "parameters specific to paired end reads": { + "title": "Parameters specific to paired end reads", + "type": "object", + "description": "No description", + "properties": { + "paired": { + "type": "boolean", + "description": "Specify that input data contain paired-end reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "count_read_pairs": { + "type": "boolean", + "description": "Count read pairs (fragments) instead of reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "both_aligned": { + "type": "boolean", + "description": "Count read pairs (fragments) instead of reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "check_pe_dist": { + "type": "boolean", + "description": "Check validity of paired-end distance when counting read pairs", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_length": { + "type": "integer", + "description": "Minimum fragment/template length, 50 by default.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + }, + "max_length": { + "type": "integer", + "description": "Maximum fragment/template length, 600 by default.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `600`. " + }, + "same_strand": { + "type": "boolean", + "description": "Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "donotsort": { + "type": "boolean", + "description": "Do not sort reads in BAM/SAM input", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/read groups" + "read groups": { + "title": "Read groups", + "type": "object", + "description": "No description", + "properties": { + "by_read_group": { + "type": "boolean", + "description": "Assign reads by read group", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/long reads" + "long reads": { + "title": "Long reads", + "type": "object", + "description": "No description", + "properties": { + "long_reads": { + "type": "boolean", + "description": "Count long reads such as Nanopore and PacBio reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/assignment results for each read" + "assignment results for each read": { + "title": "Assignment results for each read", + "type": "object", + "description": "No description", + "properties": { + "detailed_results": { + "type": "string", + "format": "path", + "description": "Directory to save the detailed assignment results", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.detailed_results\"`, direction: `output`, example: `\"detailed_results\"`. ", + "default": "$id.$key.detailed_results" + }, + "detailed_results_format": { + "type": "string", + "description": "Output detailed assignment results for each read or read-pair", + "help_text": "Type: `string`, multiple: `False`, choices: ``CORE`, `SAM`, `BAM``. ", + "enum": [ + "CORE", + "SAM", + "BAM" + ] + } + } }, - - { - "$ref": "#/definitions/miscellaneous" + "miscellaneous": { + "title": "Miscellaneous", + "type": "object", + "description": "No description", + "properties": { + "max_M_op": { + "type": "integer", + "description": "Maximum number of 'M' operations allowed in a CIGAR string", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "verbose": { + "type": "boolean", + "description": "Output verbose information for debugging, such as un-matched chromosome/contig names.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/annotation" + }, + { + "$ref": "#/$defs/level of summarization" + }, + { + "$ref": "#/$defs/overlap between reads and features" + }, + { + "$ref": "#/$defs/multi-mapping reads" + }, + { + "$ref": "#/$defs/fractional counting" + }, + { + "$ref": "#/$defs/read filtering" + }, + { + "$ref": "#/$defs/strandedness" + }, + { + "$ref": "#/$defs/exon-exon junctions" + }, + { + "$ref": "#/$defs/parameters specific to paired end reads" + }, + { + "$ref": "#/$defs/read groups" + }, + { + "$ref": "#/$defs/long reads" + }, + { + "$ref": "#/$defs/assignment results for each read" + }, + { + "$ref": "#/$defs/miscellaneous" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index 4554d5c9..7099492f 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -193,9 +193,9 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -220,6 +220,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 11d63f7e..ec4cc831 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3262,9 +3262,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq_subsample", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3280,6 +3280,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/fq_subsample/nextflow_schema.json b/target/nextflow/fq_subsample/nextflow_schema.json index 83a6f613..25e23e9b 100644 --- a/target/nextflow/fq_subsample/nextflow_schema.json +++ b/target/nextflow/fq_subsample/nextflow_schema.json @@ -1,160 +1,97 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "fq_subsample", -"description": "fq subsample outputs a subset of records from single or paired FASTQ files.", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input_1": { - "type": - "string", - "description": "Type: `file`, required. First input fastq file to subsample", - "help_text": "Type: `file`, required. First input fastq file to subsample. Accepts both raw and gzipped FASTQ inputs." - - } - - - , - "input_2": { - "type": - "string", - "description": "Type: `file`. Second input fastq files to subsample", - "help_text": "Type: `file`. Second input fastq files to subsample. Accepts both raw and gzipped FASTQ inputs." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files", - "help_text": "Type: `file`, default: `$id.$key.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`." - , - "default":"$id.$key.output_1" - } - - - , - "output_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files", - "help_text": "Type: `file`, default: `$id.$key.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`." - , - "default":"$id.$key.output_2" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "probability": { - "type": - "number", - "description": "Type: `double`. The probability a record is kept, as a percentage (0", - "help_text": "Type: `double`. The probability a record is kept, as a percentage (0.0, 1.0). Cannot be used with `record-count`" - - } - - - , - "record_count": { - "type": - "integer", - "description": "Type: `integer`. The exact number of records to keep", - "help_text": "Type: `integer`. The exact number of records to keep. Cannot be used with `probability`" - - } - - - , - "seed": { - "type": - "integer", - "description": "Type: `integer`. Seed to use for the random number generator", - "help_text": "Type: `integer`. Seed to use for the random number generator" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "fq_subsample", + "description": "fq subsample outputs a subset of records from single or paired FASTQ files.", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input_1": { + "type": "string", + "format": "path", + "exists": true, + "description": "First input fastq file to subsample", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "input_2": { + "type": "string", + "format": "path", + "description": "Second input fastq files to subsample", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output_1": { + "type": "string", + "format": "path", + "description": "Sampled read 1 fastq files", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_1\"`, direction: `output`. ", + "default": "$id.$key.output_1" + }, + "output_2": { + "type": "string", + "format": "path", + "description": "Sampled read 2 fastq files", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_2\"`, direction: `output`. ", + "default": "$id.$key.output_2" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "probability": { + "type": "number", + "description": "The probability a record is kept, as a percentage (0.0, 1.0)", + "help_text": "Type: `double`, multiple: `False`. " + }, + "record_count": { + "type": "integer", + "description": "The exact number of records to keep", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "seed": { + "type": "integer", + "description": "Seed to use for the random number generator", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index bd42c0e7..a1cd59f3 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -688,9 +683,9 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -715,6 +710,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 6c55f9be..b0b2aac6 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3044,17 +3044,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3836,9 +3828,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3854,6 +3846,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/gffread/nextflow_schema.json b/target/nextflow/gffread/nextflow_schema.json index 5ed6b228..86344854 100644 --- a/target/nextflow/gffread/nextflow_schema.json +++ b/target/nextflow/gffread/nextflow_schema.json @@ -1,816 +1,467 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "gffread", -"description": "Validate, filter, convert and perform various other operations on GFF files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `annotation.gff`. A reference file in either the GFF3, GFF2 or GTF format", - "help_text": "Type: `file`, required, example: `annotation.gff`. A reference file in either the GFF3, GFF2 or GTF format.\n" - - } - - - , - "chr_mapping": { - "type": - "string", - "description": "Type: `file`. \u003cchr_replace\u003e is a name mapping table for converting reference sequence names, \nhaving this 2-column format: \u003coriginal_ref_ID\u003e \u003cnew_ref_ID\u003e", - "help_text": "Type: `file`. \u003cchr_replace\u003e is a name mapping table for converting reference sequence names, \nhaving this 2-column format: \u003coriginal_ref_ID\u003e \u003cnew_ref_ID\u003e.\n" - - } - - - , - "seq_info": { - "type": - "string", - "description": "Type: `file`. \u003cseq_info", - "help_text": "Type: `file`. \u003cseq_info.fsize\u003e is a tab-delimited file providing this info for each of the mapped \nsequences: \u003cseq-name\u003e \u003cseq-length\u003e \u003cseq-description\u003e (useful for --description option with \nmRNA/EST/protein mappings).\n" - - } - - - , - "genome": { - "type": - "string", - "description": "Type: `file`, example: `genome.fa`. Full path to a multi-fasta file with the genomic sequences for all input mappings, \nOR a directory with single-fasta files (one per genomic sequence, with file names \nmatching sequence names)", - "help_text": "Type: `file`, example: `genome.fa`. Full path to a multi-fasta file with the genomic sequences for all input mappings, \nOR a directory with single-fasta files (one per genomic sequence, with file names \nmatching sequence names).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "outfile": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e", - "help_text": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e.\n" - , - "default":"$id.$key.outfile.gff" - } - - - , - "force_exons": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features", - "help_text": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features.\n" - , - "default":false - } - - - , - "gene2exon": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript)", - "help_text": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript).\n" - , - "default":false - } - - - , - "t_adopt": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent", - "help_text": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent.\n" - , - "default":false - } - - - , - "decode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes", - "help_text": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes.\n" - , - "default":false - } - - - , - "merge_exons": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4)", - "help_text": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4).\n" - , - "default":false - } - - - , - "junctions": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts", - "help_text": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts.\n" - , - "default":false - } - - - , - "spliced_exons": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript", - "help_text": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript.\n" - , - "default":"$id.$key.spliced_exons.fa" - } - - - , - "w_add": { - "type": - "integer", - "description": "Type: `integer`. For the --spliced_exons option, extract additional \u003cN\u003e bases both upstream and \ndownstream of the transcript boundaries", - "help_text": "Type: `integer`. For the --spliced_exons option, extract additional \u003cN\u003e bases both upstream and \ndownstream of the transcript boundaries.\n" - - } - - - , - "w_nocds": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file", - "help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file.\n" - , - "default":false - } - - - , - "spliced_cds": { - "type": - "string", - "description": "Type: `file`, example: `cds.fa`. Write a fasta file with spliced CDS for each GFF transcript", - "help_text": "Type: `file`, example: `cds.fa`. Write a fasta file with spliced CDS for each GFF transcript.\n" - - } - - - , - "tr_cds": { - "type": - "string", - "description": "Type: `file`, example: `tr_cds.fa`. Write a protein fasta file with the translation of CDS for each record", - "help_text": "Type: `file`, example: `tr_cds.fa`. Write a protein fasta file with the translation of CDS for each record.\n" - - } - - - , - "w_coords": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence", - "help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n" - , - "default":false - } - - - , - "stop_dot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027", - "help_text": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027.\u0027 as stop codon translation.\n" - , - "default":false - } - - - , - "id_version": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs", - "help_text": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs.\n" - , - "default":false - } - - - , - "trackname": { - "type": - "string", - "description": "Type: `string`. Use \u003ctrackname\u003e in the 2nd column of each GFF/GTF output line", - "help_text": "Type: `string`. Use \u003ctrackname\u003e in the 2nd column of each GFF/GTF output line.\n" - - } - - - , - "gtf_output": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3", - "help_text": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3.\n" - , - "default":false - } - - - , - "bed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3", - "help_text": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3.\n" - , - "default":false - } - - - , - "tlf": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e", - "help_text": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e.\n" - , - "default":false - } - - - , - "table": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Output a simple tab delimited format instead of GFF, with columns having the values \nof GFF attributes given in \u003cattrlist\u003e; special pseudo-attributes (prefixed by @) are \nrecognized:\n @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\nIf any of --spliced_exons/--tr_cds/--spliced_cds FASTA output files are enabled, the \nsame fields (excluding @id) are appended to the definition line of corresponding FASTA\nrecords", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Output a simple tab delimited format instead of GFF, with columns having the values \nof GFF attributes given in \u003cattrlist\u003e; special pseudo-attributes (prefixed by @) are \nrecognized:\n @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\nIf any of --spliced_exons/--tr_cds/--spliced_cds FASTA output files are enabled, the \nsame fields (excluding @id) are appended to the definition line of corresponding FASTA\nrecords.\n" - - } - - - , - "expose_dups": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records", - "help_text": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records.\n" - , - "default":false - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "ids": { - "type": - "string", - "description": "Type: `file`. Discard records/transcripts if their IDs are not listed in \u003cIDs", - "help_text": "Type: `file`. Discard records/transcripts if their IDs are not listed in \u003cIDs.lst\u003e.\n" - - } - - - , - "nids": { - "type": - "string", - "description": "Type: `file`. Discard records/transcripts if their IDs are listed in \u003cIDs", - "help_text": "Type: `file`. Discard records/transcripts if their IDs are listed in \u003cIDs.lst\u003e.\n" - - } - - - , - "maxintron": { - "type": - "integer", - "description": "Type: `integer`. Discard transcripts having an intron larger than \u003cmaxintron\u003e", - "help_text": "Type: `integer`. Discard transcripts having an intron larger than \u003cmaxintron\u003e.\n" - - } - - - , - "minlen": { - "type": - "integer", - "description": "Type: `integer`. Discard transcripts shorter than \u003cminlen\u003e bases", - "help_text": "Type: `integer`. Discard transcripts shorter than \u003cminlen\u003e bases.\n" - - } - - - , - "range": { - "type": - "string", - "description": "Type: `string`. Only show transcripts overlapping coordinate range \u003cstart\u003e", - "help_text": "Type: `string`. Only show transcripts overlapping coordinate range \u003cstart\u003e..\u003cend\u003e (on chromosome/contig \n\u003cchr\u003e, strand \u003cstrand\u003e if provided).\n" - - } - - - , - "strict_range": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange", - "help_text": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange.\n" - , - "default":false - } - - - , - "jmatch": { - "type": - "string", - "description": "Type: `string`. Only output transcripts matching the given junction", - "help_text": "Type: `string`. Only output transcripts matching the given junction.\n" - - } - - - , - "no_single_exon": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts", - "help_text": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts.\n" - , - "default":false - } - - - , - "coding": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features", - "help_text": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features.\n" - , - "default":false - } - - - , - "nc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features", - "help_text": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features.\n" - , - "default":false - } - - - , - "ignore_locus": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input", - "help_text": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input.\n" - , - "default":false - } - - - , - "description": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info", - "help_text": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info.fsize\u003e and add it as the value for a \u0027descr\u0027 \nattribute to the GFF record.\n" - , - "default":false - } - - -} -}, - - - "sorting" : { - "title": "Sorting", - "type": "object", - "description": "No description", - "properties": { - - - "sort_alpha": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically", - "help_text": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically.\n" - , - "default":false - } - - - , - "sort_by": { - "type": - "string", - "description": "Type: `file`. Sort the reference sequences by the order in which their names are given in the \n\u003crefseq", - "help_text": "Type: `file`. Sort the reference sequences by the order in which their names are given in the \n\u003crefseq.lst\u003e file.\n" - - } - - -} -}, - - - "misc options" : { - "title": "Misc options", - "type": "object", - "description": "No description", - "properties": { - - - "keep_attrs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features)", - "help_text": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features).\n" - , - "default":false - } - - - , - "keep_exon_attrs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes", - "help_text": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes.\n" - , - "default":false - } - - - , - "no_exon_attrs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output)", - "help_text": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output).\n" - , - "default":false - } - - - , - "attrs": { - "type": - "string", - "description": "Type: `string`. Only output the GTF/GFF attributes listed in \u003cattr-list\u003e which is a comma delimited \nlist of attribute names to", - "help_text": "Type: `string`. Only output the GTF/GFF attributes listed in \u003cattr-list\u003e which is a comma delimited \nlist of attribute names to.\n" - - } - - - , - "keep_genes": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records", - "help_text": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records.\n" - , - "default":false - } - - - , - "keep_comments": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments", - "help_text": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments.\n" - , - "default":false - } - - - , - "process_other": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored)", - "help_text": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored).\n" - , - "default":false - } - - - , - "rm_stop_codons": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome)", - "help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome).\n" - , - "default":false - } - - - , - "adj_cds_start": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon", - "help_text": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon.\n" - , - "default":false - } - - - , - "opposite_strand": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome)", - "help_text": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome). \n" - , - "default":false - } - - - , - "coding_status": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome)", - "help_text": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome).\n" - , - "default":false - } - - - , - "add_hasCDS": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features", - "help_text": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features. \n" - , - "default":false - } - - - , - "adj_stop": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream", - "help_text": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream.\n" - , - "default":false - } - - - , - "rm_noncanon": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i", - "help_text": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i.e. not GT-AG, GC-AG or AT-AC).\n" - , - "default":false - } - - - , - "complete_cds": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i", - "help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i.e. only print mRNAs with a complete CDS).\n" - , - "default":false - } - - - , - "no_pseudo": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword", - "help_text": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword.\n" - , - "default":false - } - - - , - "in_bed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with ", - "help_text": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with .bed*).\n" - , - "default":false - } - - - , - "in_tlf": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with ", - "help_text": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n" - , - "default":false - } - - - , - "stream": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data)", - "help_text": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data).\n" - , - "default":false - } - - -} -}, - - - "clustering" : { - "title": "Clustering", - "type": "object", - "description": "No description", - "properties": { - - - "merge": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries)", - "help_text": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries).\n" - , - "default":false - } - - - , - "dupinfo": { - "type": - "string", - "description": "Type: `file`. For --merge option, write duplication info to file \u003cdupinfo\u003e", - "help_text": "Type: `file`. For --merge option, write duplication info to file \u003cdupinfo\u003e.\n" - - } - - - , - "cluster_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features", - "help_text": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features.\n" - , - "default":false - } - - - , - "rm_redundant": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container)", - "help_text": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container).\n" - , - "default":false - } - - - , - "no_boundary": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts", - "help_text": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts.\n" - , - "default":false - } - - - , - "no_overlap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant)", - "help_text": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant).\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "gffread", + "description": "Validate, filter, convert and perform various other operations on GFF files.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "A reference file in either the GFF3, GFF2 or GTF format.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"annotation.gff\"`. " + }, + "chr_mapping": { + "type": "string", + "format": "path", + "description": " is a name mapping table for converting reference sequence names, \nhaving this 2-column format: .\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "seq_info": { + "type": "string", + "format": "path", + "description": " is a tab-delimited file providing this info for each of the mapped \nsequences: (useful for --description option with \nmRNA/EST/protein mappings).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "genome": { + "type": "string", + "format": "path", + "description": "Full path to a multi-fasta file with the genomic sequences for all input mappings, \nOR a directory with single-fasta files (one per genomic sequence, with file names \nmatching sequence names).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fa\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "outfile": { + "type": "string", + "format": "path", + "description": "Write the output records into .\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.outfile.gff\"`, direction: `output`, example: `\"output.gff\"`. ", + "default": "$id.$key.outfile.gff" + }, + "force_exons": { + "type": "boolean", + "description": "Make sure that the lowest level GFF features are considered \"exon\" features.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gene2exon": { + "type": "boolean", + "description": "For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "t_adopt": { + "type": "boolean", + "description": "Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "decode": { + "type": "boolean", + "description": "Decode url encoded characters within attributes.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "merge_exons": { + "type": "boolean", + "description": "Merge very close exons into a single exon (when intron size<4).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "junctions": { + "type": "boolean", + "description": "Output the junctions and the corresponding transcripts.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "spliced_exons": { + "type": "string", + "format": "path", + "description": "Write a fasta file with spliced exons for each transcript.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.spliced_exons.fa\"`, direction: `output`, example: `\"exons.fa\"`. ", + "default": "$id.$key.spliced_exons.fa" + }, + "w_add": { + "type": "integer", + "description": "For the --spliced_exons option, extract additional bases both upstream and \ndownstream of the transcript boundaries.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "w_nocds": { + "type": "boolean", + "description": "For --spliced_exons, disable the output of CDS info in the FASTA file.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "spliced_cds": { + "type": "string", + "format": "path", + "description": "Write a fasta file with spliced CDS for each GFF transcript.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"cds.fa\"`. " + }, + "tr_cds": { + "type": "string", + "format": "path", + "description": "Write a protein fasta file with the translation of CDS for each record.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"tr_cds.fa\"`. " + }, + "w_coords": { + "type": "boolean", + "description": "For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "stop_dot": { + "type": "boolean", + "description": "For --tr_cds option, use '*' instead of '.' as stop codon translation.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "id_version": { + "type": "boolean", + "description": "Ensembl GTF to GFF3 conversion, adds version to IDs.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "trackname": { + "type": "string", + "description": "Use in the 2nd column of each GFF/GTF output line.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "gtf_output": { + "type": "boolean", + "description": "Main output will be GTF instead of GFF3.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bed": { + "type": "boolean", + "description": "Output records in BED format instead of default GFF3.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "tlf": { + "type": "boolean", + "description": "Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=;CDSphase=;CDS=\n is a comma-delimited list of exon_start-exon_end coordinates;\n is CDS_start:CDS_end coordinates or a list like .\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "table": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Output a simple tab delimited format instead of GFF, with columns having the values \nof GFF attributes given in ; special pseudo-attributes (prefixed by @) are \nrecognized:\n @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\nIf any of --spliced_exons/--tr_cds/--spliced_cds FASTA output files are enabled, the \nsame fields (excluding @id) are appended to the definition line of corresponding FASTA\nrecords.\n", + "help_text": "Type: `string`, multiple: `True`. " + }, + "expose_dups": { + "type": "boolean", + "description": "Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "ids": { + "type": "string", + "format": "path", + "description": "Discard records/transcripts if their IDs are not listed in .\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "nids": { + "type": "string", + "format": "path", + "description": "Discard records/transcripts if their IDs are listed in .\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "maxintron": { + "type": "integer", + "description": "Discard transcripts having an intron larger than .\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "minlen": { + "type": "integer", + "description": "Discard transcripts shorter than bases.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "range": { + "type": "string", + "description": "Only show transcripts overlapping coordinate range .. (on chromosome/contig \n, strand if provided).\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "strict_range": { + "type": "boolean", + "description": "For --range option, discard all transcripts that are not fully contained within the given \nrange.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "jmatch": { + "type": "string", + "description": "Only output transcripts matching the given junction.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_single_exon": { + "type": "boolean", + "description": "Discard single-exon transcripts.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "coding": { + "type": "boolean", + "description": "Coding only: discard mRNAs that have no CDS features.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "nc": { + "type": "boolean", + "description": "Non-coding only: discard mRNAs that have CDS features.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ignore_locus": { + "type": "boolean", + "description": "Discard locus features and attributes found in the input.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "description": { + "type": "boolean", + "description": "Use the description field from and add it as the value for a 'descr' \nattribute to the GFF record.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/sorting" + "sorting": { + "title": "Sorting", + "type": "object", + "description": "No description", + "properties": { + "sort_alpha": { + "type": "boolean", + "description": "Chromosomes (reference sequences) are sorted alphabetically.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sort_by": { + "type": "string", + "format": "path", + "description": "Sort the reference sequences by the order in which their names are given in the \n file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/misc options" + "misc options": { + "title": "Misc options", + "type": "object", + "description": "No description", + "properties": { + "keep_attrs": { + "type": "boolean", + "description": "Keep all GFF attributes (for non-exon features).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep_exon_attrs": { + "type": "boolean", + "description": "For -F option, do not attempt to reduce redundant exon/CDS attributes.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_exon_attrs": { + "type": "boolean", + "description": "Do not keep exon attributes, move them to the transcript feature (for GFF3 output).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "attrs": { + "type": "string", + "description": "Only output the GTF/GFF attributes listed in which is a comma delimited \nlist of attribute names to.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "keep_genes": { + "type": "boolean", + "description": "In transcript-only mode (default), also preserve gene records.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep_comments": { + "type": "boolean", + "description": "For GFF3 input/output, try to preserve comments.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "process_other": { + "type": "boolean", + "description": "process other non-transcript GFF records (by default non-transcript records are ignored).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "rm_stop_codons": { + "type": "boolean", + "description": "Discard any mRNAs with CDS having in-frame stop codons (requires --genome).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "adj_cds_start": { + "type": "boolean", + "description": "For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "opposite_strand": { + "type": "boolean", + "description": "For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "coding_status": { + "type": "boolean", + "description": "Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "add_hasCDS": { + "type": "boolean", + "description": "Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "adj_stop": { + "type": "boolean", + "description": "Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "rm_noncanon": { + "type": "boolean", + "description": "Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "complete_cds": { + "type": "boolean", + "description": "Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_pseudo": { + "type": "boolean", + "description": "Filter out records matching the 'pseudo' keyword.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "in_bed": { + "type": "boolean", + "description": "Input should be parsed as BED format (automatic if the input filename ends with .bed*).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "in_tlf": { + "type": "boolean", + "description": "Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "stream": { + "type": "boolean", + "description": "Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/clustering" + "clustering": { + "title": "Clustering", + "type": "object", + "description": "No description", + "properties": { + "merge": { + "type": "boolean", + "description": "Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dupinfo": { + "type": "string", + "format": "path", + "description": "For --merge option, write duplication info to file .\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "cluster_only": { + "type": "boolean", + "description": "Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "rm_redundant": { + "type": "boolean", + "description": "For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_boundary": { + "type": "boolean", + "description": "For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and >=80%\noverlap for single-exon transcripts.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_overlap": { + "type": "boolean", + "description": "For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/sorting" + }, + { + "$ref": "#/$defs/misc options" + }, + { + "$ref": "#/$defs/clustering" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index b5a946e4..a00e15fb 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -221,9 +221,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -248,6 +248,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index f30f2ab5..23305a46 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3301,9 +3301,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3319,6 +3319,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json index 44e9e575..06a4fa0b 100644 --- a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json @@ -1,192 +1,113 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "kallisto_index", -"description": "Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Path to a FASTA-file containing the transcriptome sequences, either in plain text or \ncompressed (", - "help_text": "Type: `file`, required. Path to a FASTA-file containing the transcriptome sequences, either in plain text or \ncompressed (.gz) format.\n" - - } - - - , - "d_list": { - "type": - "string", - "description": "Type: `file`. Path to a FASTA-file containing sequences to mask from quantification", - "help_text": "Type: `file`. Path to a FASTA-file containing sequences to mask from quantification.\n" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. ", - "help_text": "Type: `file`, default: `$id.$key.index`, example: `Kallisto_index`. " - , - "default":"$id.$key.index" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "kmer_size": { - "type": - "integer", - "description": "Type: `integer`, example: `31`. Kmer length passed to indexing step of pseudoaligners (default: \u002731\u0027)", - "help_text": "Type: `integer`, example: `31`. Kmer length passed to indexing step of pseudoaligners (default: \u002731\u0027).\n" - - } - - - , - "make_unique": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names", - "help_text": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names.\n" - , - "default":false - } - - - , - "aa": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences", - "help_text": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences.\n" - , - "default":false - } - - - , - "distiguish": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names", - "help_text": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names.\n" - , - "default":false - } - - - , - "min_size": { - "type": - "integer", - "description": "Type: `integer`. Length of minimizers (default: automatically chosen)", - "help_text": "Type: `integer`. Length of minimizers (default: automatically chosen).\n" - - } - - - , - "ec_max_size": { - "type": - "integer", - "description": "Type: `integer`. Maximum number of targets in an equivalence class (default: no maximum)", - "help_text": "Type: `integer`. Maximum number of targets in an equivalence class (default: no maximum).\n" - - } - - - , - "tmp": { - "type": - "string", - "description": "Type: `string`, example: `tmp`. Path to a directory for temporary files", - "help_text": "Type: `string`, example: `tmp`. Path to a directory for temporary files.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "kallisto_index", + "description": "Build a Kallisto index for the transcriptome to use Kallisto in the mapping-based mode.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Path to a FASTA-file containing the transcriptome sequences, either in plain text or \ncompressed (.gz) format.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "d_list": { + "type": "string", + "format": "path", + "description": "Path to a FASTA-file containing sequences to mask from quantification.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "string", + "format": "path", + "description": "", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.index\"`, direction: `output`, example: `\"Kallisto_index\"`. ", + "default": "$id.$key.index" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "kmer_size": { + "type": "integer", + "description": "Kmer length passed to indexing step of pseudoaligners (default: '31').\n", + "help_text": "Type: `integer`, multiple: `False`, example: `31`. " + }, + "make_unique": { + "type": "boolean", + "description": "Replace repeated target names with unique names.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "aa": { + "type": "boolean", + "description": "Generate index from a FASTA-file containing amino acid sequences.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "distiguish": { + "type": "boolean", + "description": "Generate index where sequences are distinguished by the sequence names.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_size": { + "type": "integer", + "description": "Length of minimizers (default: automatically chosen).\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "ec_max_size": { + "type": "integer", + "description": "Maximum number of targets in an equivalence class (default: no maximum).\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "tmp": { + "type": "string", + "description": "Path to a directory for temporary files.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"tmp\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 1e1551ba..240216a9 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -249,9 +249,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -276,6 +276,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 3a3d825a..721c2148 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3335,9 +3335,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3353,6 +3353,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json index 384e1537..ad4e29c5 100644 --- a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json @@ -1,225 +1,136 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "kallisto_quant", -"description": "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, multiple_sep: `\";\"`. List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively", - "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively." - - } - - - , - "index": { - "type": - "string", - "description": "Type: `file`, required. Kallisto genome index", - "help_text": "Type: `file`, required. Kallisto genome index." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_dir": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to", - "help_text": "Type: `file`, required, default: `$id.$key.output_dir`. Directory to write output to." - , - "default":"$id.$key.output_dir" - } - - - , - "log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant", - "help_text": "Type: `file`, default: `$id.$key.log`. File containing log information from running kallisto quant" - , - "default":"$id.$key.log" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "single": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Single end mode", - "help_text": "Type: `boolean_true`, default: `false`. Single end mode." - , - "default":false - } - - - , - "single_overhang": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript", - "help_text": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript." - , - "default":false - } - - - , - "fr_stranded": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward", - "help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward." - , - "default":false - } - - - , - "rf_stranded": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse", - "help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse." - , - "default":false - } - - - , - "fragment_length": { - "type": - "number", - "description": "Type: `double`. The estimated average fragment length", - "help_text": "Type: `double`. The estimated average fragment length." - - } - - - , - "sd": { - "type": - "number", - "description": "Type: `double`. The estimated standard deviation of the fragment length (default: -l, -s values are estimated \nfrom paired end data, but are required when using --single)", - "help_text": "Type: `double`. The estimated standard deviation of the fragment length (default: -l, -s values are estimated \nfrom paired end data, but are required when using --single).\n" - - } - - - , - "plaintext": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5", - "help_text": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5." - , - "default":false - } - - - , - "bootstrap_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Number of bootstrap samples to draw", - "help_text": "Type: `integer`, example: `0`. Number of bootstrap samples to draw. Default: \u00270\u0027\n" - - } - - - , - "seed": { - "type": - "integer", - "description": "Type: `integer`, example: `42`. Random seed for bootstrap", - "help_text": "Type: `integer`, example: `42`. Random seed for bootstrap. Default: \u002742\u0027\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "kallisto_quant", + "description": "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. " + }, + "index": { + "type": "string", + "format": "path", + "exists": true, + "description": "Kallisto genome index.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output_dir": { + "type": "string", + "format": "path", + "description": "Directory to write output to.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_dir\"`, direction: `output`. ", + "default": "$id.$key.output_dir" + }, + "log": { + "type": "string", + "format": "path", + "description": "File containing log information from running kallisto quant", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log\"`, direction: `output`. ", + "default": "$id.$key.log" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "single": { + "type": "boolean", + "description": "Single end mode.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "single_overhang": { + "type": "boolean", + "description": "Include reads where unobserved rest of fragment is predicted to lie outside a transcript.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fr_stranded": { + "type": "boolean", + "description": "Strand specific reads, first read forward.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "rf_stranded": { + "type": "boolean", + "description": "Strand specific reads, first read reverse.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fragment_length": { + "type": "number", + "description": "The estimated average fragment length.", + "help_text": "Type: `double`, multiple: `False`. " + }, + "sd": { + "type": "number", + "description": "The estimated standard deviation of the fragment length (default: -l, -s values are estimated \nfrom paired end data, but are required when using --single).\n", + "help_text": "Type: `double`, multiple: `False`. " + }, + "plaintext": { + "type": "boolean", + "description": "Output plaintext instead of HDF5.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bootstrap_samples": { + "type": "integer", + "description": "Number of bootstrap samples to draw", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "seed": { + "type": "integer", + "description": "Random seed for bootstrap", + "help_text": "Type: `integer`, multiple: `False`, example: `42`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 0834ab31..7a130518 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -8,17 +8,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -510,9 +502,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -537,6 +529,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index d2fc2d66..c2acd07f 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3045,23 +3045,10 @@ meta = [ ], "info" : { "links" : { - "email" : "kai@data-intuitive.com", "github" : "KaiWaldrant", "orcid" : "0009-0003-8555-1361", "linkedin" : "kaiwaldrant" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Contributor" - } - ] + } } } ], @@ -3644,9 +3631,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3662,6 +3649,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/lofreq/lofreq_call/nextflow_schema.json b/target/nextflow/lofreq/lofreq_call/nextflow_schema.json index da924c4f..182af833 100644 --- a/target/nextflow/lofreq/lofreq_call/nextflow_schema.json +++ b/target/nextflow/lofreq/lofreq_call/nextflow_schema.json @@ -1,454 +1,255 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "lofreq_call", -"description": "Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.\n\nLoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `normal.bam`. Input BAM file", - "help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n" - - } - - - , - "input_bai": { - "type": - "string", - "description": "Type: `file`, required, example: `normal.bai`. Index file for the input BAM file", - "help_text": "Type: `file`, required, example: `normal.bai`. Index file for the input BAM file.\n" - - } - - - , - "ref": { - "type": - "string", - "description": "Type: `file`, required, example: `reference.fasta`. Indexed reference fasta file (gzip supported)", - "help_text": "Type: `file`, required, example: `reference.fasta`. Indexed reference fasta file (gzip supported). Default: none.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "out": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.out.vcf`, example: `output.vcf`. Vcf output file", - "help_text": "Type: `file`, required, default: `$id.$key.out.vcf`, example: `output.vcf`. Vcf output file. Default: stdout.\n" - , - "default":"$id.$key.out.vcf" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "region": { - "type": - "string", - "description": "Type: `string`, example: `chr1:1000-2000`. Limit calls to this region (chrom:start-end)", - "help_text": "Type: `string`, example: `chr1:1000-2000`. Limit calls to this region (chrom:start-end). Default: none.\n" - - } - - - , - "bed": { - "type": - "string", - "description": "Type: `file`, example: `regions.bed`. List of positions (chr pos) or regions (BED)", - "help_text": "Type: `file`, example: `regions.bed`. List of positions (chr pos) or regions (BED). Default: none.\n" - - } - - - , - "min_bq": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. Skip any base with baseQ smaller than INT", - "help_text": "Type: `integer`, example: `6`. Skip any base with baseQ smaller than INT. Default: 6.\n" - - } - - - , - "min_alt_bq": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. Skip alternate bases with baseQ smaller than INT", - "help_text": "Type: `integer`, example: `6`. Skip alternate bases with baseQ smaller than INT. Default: 6.\n" - - } - - - , - "def_alt_bq": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep)", - "help_text": "Type: `integer`, example: `0`. Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.\n" - - } - - - , - "min_jq": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Skip any base with joinedQ smaller than INT", - "help_text": "Type: `integer`, example: `0`. Skip any base with joinedQ smaller than INT. Default: 0.\n" - - } - - - , - "min_alt_jq": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Skip alternate bases with joinedQ smaller than INT", - "help_text": "Type: `integer`, example: `0`. Skip alternate bases with joinedQ smaller than INT. Default: 0.\n" - - } - - - , - "def_alt_jq": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)", - "help_text": "Type: `integer`, example: `0`. Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep). Default: 0.\n" - - } - - - , - "no_baq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable use of base-alignment quality (BAQ)", - "help_text": "Type: `boolean_true`, default: `false`. Disable use of base-alignment quality (BAQ).\n" - , - "default":false - } - - - , - "no_idaq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t use IDAQ values (NOT recommended under ANY circumstances other than debugging)", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t use IDAQ values (NOT recommended under ANY circumstances other than debugging).\n" - , - "default":false - } - - - , - "del_baq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Delete pre-existing BAQ values, i", - "help_text": "Type: `boolean_true`, default: `false`. Delete pre-existing BAQ values, i.e. compute even if already present in BAM.\n" - , - "default":false - } - - - , - "no_ext_baq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use \u0027normal\u0027 BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)", - "help_text": "Type: `boolean_true`, default: `false`. Use \u0027normal\u0027 BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag).\n" - , - "default":false - } - - - , - "min_mq": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Skip reads with mapping quality smaller than INT", - "help_text": "Type: `integer`, example: `0`. Skip reads with mapping quality smaller than INT. Default: 0.\n" - - } - - - , - "max_mq": { - "type": - "integer", - "description": "Type: `integer`, example: `255`. Cap mapping quality at INT", - "help_text": "Type: `integer`, example: `255`. Cap mapping quality at INT. Default: 255.\n" - - } - - - , - "no_mq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t merge mapping quality in LoFreq\u0027s model", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t merge mapping quality in LoFreq\u0027s model.\n" - , - "default":false - } - - - , - "call_indels": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable indel calls (note: preprocess your file to include indel alignment qualities!)", - "help_text": "Type: `boolean_true`, default: `false`. Enable indel calls (note: preprocess your file to include indel alignment qualities!).\n" - , - "default":false - } - - - , - "only_indels": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only call indels; no SNVs", - "help_text": "Type: `boolean_true`, default: `false`. Only call indels; no SNVs.\n" - , - "default":false - } - - - , - "src_qual": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable computation of source quality", - "help_text": "Type: `boolean_true`, default: `false`. Enable computation of source quality.\n" - , - "default":false - } - - - , - "ign_vcf": { - "type": - "string", - "description": "Type: `file`, example: `variants.vcf`. Ignore variants in this vcf file for source quality computation", - "help_text": "Type: `file`, example: `variants.vcf`. Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas.\n" - - } - - - , - "def_nm_q": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. If \u003e= 0, then replace non-match base qualities with this default value", - "help_text": "Type: `integer`, example: `-1`. If \u003e= 0, then replace non-match base qualities with this default value. Default: -1.\n" - - } - - - , - "sig": { - "type": - "number", - "description": "Type: `double`, example: `0.01`. P-Value cutoff / significance level", - "help_text": "Type: `double`, example: `0.01`. P-Value cutoff / significance level. Default: 0.010000.\n" - - } - - - , - "bonf": { - "type": - "string", - "description": "Type: `string`, example: `dynamic`. Bonferroni factor", - "help_text": "Type: `string`, example: `dynamic`. Bonferroni factor. \u0027dynamic\u0027 (increase per actually performed test) or INT. Default: Dynamic.\n" - - } - - - , - "min_cov": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Test only positions having at least this coverage", - "help_text": "Type: `integer`, example: `1`. Test only positions having at least this coverage. Default: 1.\n(note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done).\n" - - } - - - , - "max_depth": { - "type": - "integer", - "description": "Type: `integer`, example: `1000000`. Cap coverage at this depth", - "help_text": "Type: `integer`, example: `1000000`. Cap coverage at this depth. Default: 1000000.\n" - - } - - - , - "illumina_13": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Assume the quality is Illumina-1", - "help_text": "Type: `boolean_true`, default: `false`. Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.\n" - , - "default":false - } - - - , - "use_orphan": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Count anomalous read pairs (i", - "help_text": "Type: `boolean_true`, default: `false`. Count anomalous read pairs (i.e. where mate is not aligned properly).\n" - , - "default":false - } - - - , - "plp_summary_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. No variant calling", - "help_text": "Type: `boolean_true`, default: `false`. No variant calling. Just output pileup summary per column.\n" - , - "default":false - } - - - , - "no_default_filter": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t run default \u0027lofreq filter\u0027 automatically after calling variants", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t run default \u0027lofreq filter\u0027 automatically after calling variants.\n" - , - "default":false - } - - - , - "force_overwrite": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Overwrite any existing output", - "help_text": "Type: `boolean_true`, default: `false`. Overwrite any existing output.\n" - , - "default":false - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Be verbose", - "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n" - , - "default":false - } - - - , - "debug": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable debugging", - "help_text": "Type: `boolean_true`, default: `false`. Enable debugging.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "lofreq_call", + "description": "Call variants from a BAM file.\n\nLoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.\n\nLoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.\n\nLoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BAM file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"normal.bam\"`. " + }, + "input_bai": { + "type": "string", + "format": "path", + "exists": true, + "description": "Index file for the input BAM file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"normal.bai\"`. " + }, + "ref": { + "type": "string", + "format": "path", + "exists": true, + "description": "Indexed reference fasta file (gzip supported)", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reference.fasta\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "out": { + "type": "string", + "format": "path", + "description": "Vcf output file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.out.vcf\"`, direction: `output`, example: `\"output.vcf\"`. ", + "default": "$id.$key.out.vcf" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "region": { + "type": "string", + "description": "Limit calls to this region (chrom:start-end)", + "help_text": "Type: `string`, multiple: `False`, example: `\"chr1:1000-2000\"`. " + }, + "bed": { + "type": "string", + "format": "path", + "description": "List of positions (chr pos) or regions (BED)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"regions.bed\"`. " + }, + "min_bq": { + "type": "integer", + "description": "Skip any base with baseQ smaller than INT", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "min_alt_bq": { + "type": "integer", + "description": "Skip alternate bases with baseQ smaller than INT", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "def_alt_bq": { + "type": "integer", + "description": "Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep)", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "min_jq": { + "type": "integer", + "description": "Skip any base with joinedQ smaller than INT", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "min_alt_jq": { + "type": "integer", + "description": "Skip alternate bases with joinedQ smaller than INT", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "def_alt_jq": { + "type": "integer", + "description": "Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "no_baq": { + "type": "boolean", + "description": "Disable use of base-alignment quality (BAQ).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_idaq": { + "type": "boolean", + "description": "Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "del_baq": { + "type": "boolean", + "description": "Delete pre-existing BAQ values, i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_ext_baq": { + "type": "boolean", + "description": "Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_mq": { + "type": "integer", + "description": "Skip reads with mapping quality smaller than INT", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "max_mq": { + "type": "integer", + "description": "Cap mapping quality at INT", + "help_text": "Type: `integer`, multiple: `False`, example: `255`. " + }, + "no_mq": { + "type": "boolean", + "description": "Don't merge mapping quality in LoFreq's model.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "call_indels": { + "type": "boolean", + "description": "Enable indel calls (note: preprocess your file to include indel alignment qualities!).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "only_indels": { + "type": "boolean", + "description": "Only call indels; no SNVs.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "src_qual": { + "type": "boolean", + "description": "Enable computation of source quality.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ign_vcf": { + "type": "string", + "format": "path", + "description": "Ignore variants in this vcf file for source quality computation", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"variants.vcf\"`. " + }, + "def_nm_q": { + "type": "integer", + "description": "If >= 0, then replace non-match base qualities with this default value", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "sig": { + "type": "number", + "description": "P-Value cutoff / significance level", + "help_text": "Type: `double`, multiple: `False`, example: `0.01`. " + }, + "bonf": { + "type": "string", + "description": "Bonferroni factor", + "help_text": "Type: `string`, multiple: `False`, example: `\"dynamic\"`. " + }, + "min_cov": { + "type": "integer", + "description": "Test only positions having at least this coverage", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "max_depth": { + "type": "integer", + "description": "Cap coverage at this depth", + "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. " + }, + "illumina_13": { + "type": "boolean", + "description": "Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "use_orphan": { + "type": "boolean", + "description": "Count anomalous read pairs (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "plp_summary_only": { + "type": "boolean", + "description": "No variant calling", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_default_filter": { + "type": "boolean", + "description": "Don't run default 'lofreq filter' automatically after calling variants.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "force_overwrite": { + "type": "boolean", + "description": "Overwrite any existing output.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "boolean", + "description": "Be verbose.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "debug": { + "type": "boolean", + "description": "Enable debugging.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 0386e2d6..c967b37e 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -8,17 +8,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -218,9 +210,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -245,6 +237,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index eb45011f..58e2ad68 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3045,23 +3045,10 @@ meta = [ ], "info" : { "links" : { - "email" : "kai@data-intuitive.com", "github" : "KaiWaldrant", "orcid" : "0009-0003-8555-1361", "linkedin" : "kaiwaldrant" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Contributor" - } - ] + } } } ], @@ -3307,9 +3294,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3325,6 +3312,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json index 2ee7baf6..de2272c1 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json +++ b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json @@ -1,151 +1,92 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "lofreq_indelqual", -"description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK\u0027s BQSR (\u003e=2) If that\u0027s not possible, use this subcommand.\nThe command has two modes: \u0027uniform\u0027 and \u0027dindel\u0027:\n- \u0027uniform\u0027 will assign a given value uniformly, whereas\n- \u0027dindel\u0027 will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `normal.bam`. Input BAM file", - "help_text": "Type: `file`, required, example: `normal.bam`. Input BAM file.\n" - - } - - - , - "ref": { - "type": - "string", - "description": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel)", - "help_text": "Type: `file`, example: `reference.fasta`. Reference sequence used for mapping (Only required for --dindel).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "out": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file", - "help_text": "Type: `file`, required, default: `$id.$key.out.bam`, example: `output.bam`. Output BAM file.\n" - , - "default":"$id.$key.out.bam" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "uniform": { - "type": - "string", - "description": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases", - "help_text": "Type: `string`, example: `50,50`. Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel).\n" - - } - - - , - "dindel": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref)", - "help_text": "Type: `boolean_true`, default: `false`. Add Dindel\u0027s indel qualities (Illumina specific) (clashes with -u; needs --ref).\n" - , - "default":false - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Be verbose", - "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "lofreq_indelqual", + "description": "Insert indel qualities into BAM file (required for indel predictions).\n\nThe preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand.\nThe command has two modes: 'uniform' and 'dindel':\n- 'uniform' will assign a given value uniformly, whereas\n- 'dindel' will insert indel qualities based on Dindel (PMID 20980555).\nBoth will overwrite any existing values.\nDo not realign your BAM file afterwards!\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BAM file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"normal.bam\"`. " + }, + "ref": { + "type": "string", + "format": "path", + "description": "Reference sequence used for mapping (Only required for --dindel).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"reference.fasta\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "out": { + "type": "string", + "format": "path", + "description": "Output BAM file.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.out.bam\"`, direction: `output`, example: `\"output.bam\"`. ", + "default": "$id.$key.out.bam" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "uniform": { + "type": "string", + "description": "Add this indel quality uniformly to all bases", + "help_text": "Type: `string`, multiple: `False`, example: `\"50,50\"`. " + }, + "dindel": { + "type": "boolean", + "description": "Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs --ref).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "boolean", + "description": "Be verbose.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index 35faf9b9..1e38d601 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -459,9 +459,9 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -486,6 +486,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index bcd6ab37..cdcd88d4 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3596,9 +3596,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3614,6 +3614,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/multiqc/nextflow_schema.json b/target/nextflow/multiqc/nextflow_schema.json index 04c0a3b7..fec92e4c 100644 --- a/target/nextflow/multiqc/nextflow_schema.json +++ b/target/nextflow/multiqc/nextflow_schema.json @@ -1,529 +1,334 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "multiqc", -"description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\u0027s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report", - "help_text": "Type: List of `file`, required, example: `data/results`, multiple_sep: `\";\"`. File paths to be searched for analysis results to be included in the report.\n" - - } - - -} -}, - - - "ouput" : { - "title": "Ouput", - "type": "object", - "description": "No description", - "properties": { - - - "output_report": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report", - "help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n" - , - "default":"$id.$key.output_report.html" - } - - - , - "output_data": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files", - "help_text": "Type: `file`, default: `$id.$key.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n" - , - "default":"$id.$key.output_data" - } - - - , - "output_plots": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots", - "help_text": "Type: `file`, default: `$id.$key.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n" - , - "default":"$id.$key.output_plots" - } - - -} -}, - - - "modules and analyses to run" : { - "title": "Modules and analyses to run", - "type": "object", - "description": "No description", - "properties": { - - - "include_modules": { - "type": - "string", - "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module", - "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Use only these module" - - } - - - , - "exclude_modules": { - "type": - "string", - "description": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules", - "help_text": "Type: List of `string`, example: `fastqc;cutadapt`, multiple_sep: `\";\"`. Do not use only these modules" - - } - - - , - "ignore_analysis": { - "type": - "string", - "description": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. ", - "help_text": "Type: List of `string`, example: `run_one/*;run_two/*`, multiple_sep: `\";\"`. " - - } - - - , - "ignore_samples": { - "type": - "string", - "description": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. ", - "help_text": "Type: List of `string`, example: `sample_1*;sample_3*`, multiple_sep: `\";\"`. " - - } - - - , - "ignore_symlinks": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files", - "help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files" - , - "default":false - } - - -} -}, - - - "sample name handling" : { - "title": "Sample name handling", - "type": "object", - "description": "No description", - "properties": { - - - "dirs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames", - "help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames" - , - "default":false - } - - - , - "dirs_depth": { - "type": - "integer", - "description": "Type: `integer`. Prepend n directories to sample names", - "help_text": "Type: `integer`. Prepend n directories to sample names. Negative number to take from start of path." - - } - - - , - "full_names": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)", - "help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)" - , - "default":false - } - - - , - "fn_as_s_name": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name", - "help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name" - , - "default":false - } - - - , - "replace_names": { - "type": - "string", - "description": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation", - "help_text": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation" - - } - - -} -}, - - - "report customisation" : { - "title": "Report Customisation", - "type": "object", - "description": "No description", - "properties": { - - - "title": { - "type": - "string", - "description": "Type: `string`. Report title", - "help_text": "Type: `string`. Report title. Printed as page header, used for filename if not otherwise specified.\n" - - } - - - , - "comment": { - "type": - "string", - "description": "Type: `string`. Custom comment, will be printed at the top of the report", - "help_text": "Type: `string`. Custom comment, will be printed at the top of the report.\n" - - } - - - , - "template": { - "type": - "string", - "description": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use", - "help_text": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use.\n", - "enum": ["default", "gathered", "geo", "highcharts", "sections", "simple"] - - - } - - - , - "sample_names": { - "type": - "string", - "description": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report", - "help_text": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report.\n" - - } - - - , - "sample_filters": { - "type": - "string", - "description": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n", - "help_text": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n" - - } - - - , - "custom_css_file": { - "type": - "string", - "description": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n", - "help_text": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n" - - } - - - , - "profile_runtime": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n", - "help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n" - , - "default":false - } - - -} -}, - - - "multiqc behaviour" : { - "title": "MultiQC behaviour", - "type": "object", - "description": "No description", - "properties": { - - - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Increase output verbosity", - "help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n" - , - "default":false - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only show log warnings\n", - "help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n" - , - "default":false - } - - - , - "strict": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n" - , - "default":false - } - - - , - "development": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Development mode", - "help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n" - , - "default":false - } - - - , - "require_logs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files", - "help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n" - , - "default":false - } - - - , - "no_megaqc_upload": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n" - , - "default":false - } - - - , - "no_ansi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable coloured log output", - "help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n" - , - "default":false - } - - - , - "cl_config": { - "type": - "string", - "description": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection", - "help_text": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n" - - } - - -} -}, - - - "output format" : { - "title": "Output format", - "type": "object", - "description": "No description", - "properties": { - - - "flat": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)", - "help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n" - , - "default":false - } - - - , - "interactive": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)", - "help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n" - , - "default":false - } - - - , - "data_dir": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created", - "help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n" - , - "default":false - } - - - , - "no_data_dir": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created", - "help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n" - , - "default":false - } - - - , - "zip_data_dir": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Compress the data directory", - "help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n" - , - "default":false - } - - - , - "data_format": { - "type": - "string", - "description": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027", - "help_text": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027.\n", - "enum": ["tsv", "csv", "json", "yaml"] - - - } - - - , - "pdf": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template", - "help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "multiqc", + "description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "File paths to be searched for analysis results to be included in the report.\n", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"data/results\"]`. " + } + } }, - - { - "$ref": "#/definitions/ouput" + "ouput": { + "title": "Ouput", + "type": "object", + "description": "No description", + "properties": { + "output_report": { + "type": "string", + "format": "path", + "description": "Filepath of the generated report.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_report.html\"`, direction: `output`, example: `\"multiqc_report.html\"`. ", + "default": "$id.$key.output_report.html" + }, + "output_data": { + "type": "string", + "format": "path", + "description": "Output directory for parsed data files", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_data\"`, direction: `output`, example: `\"multiqc_data\"`. ", + "default": "$id.$key.output_data" + }, + "output_plots": { + "type": "string", + "format": "path", + "description": "Output directory for generated plots", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_plots\"`, direction: `output`, example: `\"multiqc_plots\"`. ", + "default": "$id.$key.output_plots" + } + } }, - - { - "$ref": "#/definitions/modules and analyses to run" + "modules and analyses to run": { + "title": "Modules and analyses to run", + "type": "object", + "description": "No description", + "properties": { + "include_modules": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Use only these module", + "help_text": "Type: `string`, multiple: `True`, example: `[\"fastqc\";\"cutadapt\"]`. " + }, + "exclude_modules": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Do not use only these modules", + "help_text": "Type: `string`, multiple: `True`, example: `[\"fastqc\";\"cutadapt\"]`. " + }, + "ignore_analysis": { + "type": "array", + "items": { + "type": "string" + }, + "description": "", + "help_text": "Type: `string`, multiple: `True`, example: `[\"run_one/*\";\"run_two/*\"]`. " + }, + "ignore_samples": { + "type": "array", + "items": { + "type": "string" + }, + "description": "", + "help_text": "Type: `string`, multiple: `True`, example: `[\"sample_1*\";\"sample_3*\"]`. " + }, + "ignore_symlinks": { + "type": "boolean", + "description": "Ignore symlinked directories and files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/sample name handling" + "sample name handling": { + "title": "Sample name handling", + "type": "object", + "description": "No description", + "properties": { + "dirs": { + "type": "boolean", + "description": "Prepend directory to sample names to avoid clashing filenames", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dirs_depth": { + "type": "integer", + "description": "Prepend n directories to sample names", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "full_names": { + "type": "boolean", + "description": "Do not clean the sample names (leave as full file name)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fn_as_s_name": { + "type": "boolean", + "description": "Use the log filename as the sample name", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "replace_names": { + "type": "string", + "format": "path", + "description": "TSV file to rename sample names during report generation", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"replace_names.tsv\"`. " + } + } }, - - { - "$ref": "#/definitions/report customisation" + "report customisation": { + "title": "Report Customisation", + "type": "object", + "description": "No description", + "properties": { + "title": { + "type": "string", + "description": "Report title", + "help_text": "Type: `string`, multiple: `False`. " + }, + "comment": { + "type": "string", + "description": "Custom comment, will be printed at the top of the report.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "template": { + "type": "string", + "description": "Report template to use.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. ", + "enum": [ + "default", + "gathered", + "geo", + "highcharts", + "sections", + "simple" + ] + }, + "sample_names": { + "type": "string", + "format": "path", + "description": "TSV file containing alternative sample names for renaming buttons in the report.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"sample_names.tsv\"`. " + }, + "sample_filters": { + "type": "string", + "format": "path", + "description": "TSV file containing show/hide patterns for the report\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"sample_filters.tsv\"`. " + }, + "custom_css_file": { + "type": "string", + "format": "path", + "description": "Custom CSS file to add to the final report\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"custom_style_sheet.css\"`. " + }, + "profile_runtime": { + "type": "boolean", + "description": "Add analysis of how long MultiQC takes to run to the report\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/multiqc behaviour" + "multiqc behaviour": { + "title": "MultiQC behaviour", + "type": "object", + "description": "No description", + "properties": { + "verbose": { + "type": "boolean", + "description": "Increase output verbosity.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "quiet": { + "type": "boolean", + "description": "Only show log warnings\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "strict": { + "type": "boolean", + "description": "Don't catch exceptions, run additional code checks to help development.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "development": { + "type": "boolean", + "description": "Development mode", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "require_logs": { + "type": "boolean", + "description": "Require all explicitly requested modules to have log files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_megaqc_upload": { + "type": "boolean", + "description": "Don't upload generated report to MegaQC, even if MegaQC options are found.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_ansi": { + "type": "boolean", + "description": "Disable coloured log output.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "cl_config": { + "type": "string", + "description": "YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"qualimap_config: { general_stats_coverage: [20,40,200] }\"`. " + } + } }, - - { - "$ref": "#/definitions/output format" + "output format": { + "title": "Output format", + "type": "object", + "description": "No description", + "properties": { + "flat": { + "type": "boolean", + "description": "Use only flat plots (static images).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "interactive": { + "type": "boolean", + "description": "Use only interactive plots (in-browser Javascript).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "data_dir": { + "type": "boolean", + "description": "Force the parsed data directory to be created.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_data_dir": { + "type": "boolean", + "description": "Prevent the parsed data directory from being created.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "zip_data_dir": { + "type": "boolean", + "description": "Compress the data directory.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "data_format": { + "type": "string", + "description": "Output parsed data in a different format than the default 'txt'.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``tsv`, `csv`, `json`, `yaml``. ", + "enum": [ + "tsv", + "csv", + "json", + "yaml" + ] + }, + "pdf": { + "type": "boolean", + "description": "Creates PDF report with the 'simple' template", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/ouput" + }, + { + "$ref": "#/$defs/modules and analyses to run" + }, + { + "$ref": "#/$defs/sample name handling" + }, + { + "$ref": "#/$defs/report customisation" + }, + { + "$ref": "#/$defs/multiqc behaviour" + }, + { + "$ref": "#/$defs/output format" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/nanoplot/.config.vsh.yaml b/target/nextflow/nanoplot/.config.vsh.yaml index e5a6aacc..032f23eb 100644 --- a/target/nextflow/nanoplot/.config.vsh.yaml +++ b/target/nextflow/nanoplot/.config.vsh.yaml @@ -495,9 +495,9 @@ build_info: output: "target/nextflow/nanoplot" executable: "target/nextflow/nanoplot/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -522,6 +522,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/nanoplot/main.nf b/target/nextflow/nanoplot/main.nf index c68f918c..f2ef5673 100644 --- a/target/nextflow/nanoplot/main.nf +++ b/target/nextflow/nanoplot/main.nf @@ -3627,9 +3627,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/nanoplot", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3645,6 +3645,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/nanoplot/nextflow_schema.json b/target/nextflow/nanoplot/nextflow_schema.json index 74ef439f..c8e5fe26 100644 --- a/target/nextflow/nanoplot/nextflow_schema.json +++ b/target/nextflow/nanoplot/nextflow_schema.json @@ -1,587 +1,362 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "nanoplot", -"description": "Run NanoPlot on nanopore-sequenced reads.\nNanoPlot is a plotting tool for long read sequencing data and alignments.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "fastq": { - "type": - "string", - "description": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s), separated by \";\"." - - } - - - , - "fasta": { - "type": - "string", - "description": "Type: List of `file`, example: `read.fa`, multiple_sep: `\";\"`. Input fasta file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.fa`, multiple_sep: `\";\"`. Input fasta file(s), separated by \";\"." - - } - - - , - "fastq_rich": { - "type": - "string", - "description": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s) generated by albacore or \nMinKNOW with additional information concerning channel and time, separated by \";\"", - "help_text": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s) generated by albacore or \nMinKNOW with additional information concerning channel and time, separated by \";\".\n" - - } - - - , - "fastq_minimal": { - "type": - "string", - "description": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s) generated by albacore or MinKNOW with\nadditional information concerning channel and time", - "help_text": "Type: List of `file`, example: `read.fq`, multiple_sep: `\";\"`. Input fastq file(s) generated by albacore or MinKNOW with\nadditional information concerning channel and time. Minimal data is extracted\nswiftly without elaborate checks. Separated by \";\".\n" - - } - - - , - "summary": { - "type": - "string", - "description": "Type: List of `file`, example: `read.txt`, multiple_sep: `\";\"`. Input summary file(s) generated by albacore or guppy, separated by \";\"", - "help_text": "Type: List of `file`, example: `read.txt`, multiple_sep: `\";\"`. Input summary file(s) generated by albacore or guppy, separated by \";\".\n" - - } - - - , - "bam": { - "type": - "string", - "description": "Type: List of `file`, example: `read.bam`, multiple_sep: `\";\"`. Input sorted bam file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.bam`, multiple_sep: `\";\"`. Input sorted bam file(s), separated by \";\"." - - } - - - , - "ubam": { - "type": - "string", - "description": "Type: List of `file`, example: `read.ubam`, multiple_sep: `\";\"`. Input unmapped bam file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.ubam`, multiple_sep: `\";\"`. Input unmapped bam file(s), separated by \";\"." - - } - - - , - "cram": { - "type": - "string", - "description": "Type: List of `file`, example: `read.cram`, multiple_sep: `\";\"`. Input sorted cram file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.cram`, multiple_sep: `\";\"`. Input sorted cram file(s), separated by \";\"." - - } - - - , - "pickle": { - "type": - "string", - "description": "Type: List of `file`, example: `read.pkl`, multiple_sep: `\";\"`. Input pickle file stored earlier, separated by \";\"", - "help_text": "Type: List of `file`, example: `read.pkl`, multiple_sep: `\";\"`. Input pickle file stored earlier, separated by \";\"." - - } - - - , - "feather": { - "type": - "string", - "description": "Type: List of `file`, example: `read.arrow`, multiple_sep: `\";\"`. Input feather file(s), separated by \";\"", - "help_text": "Type: List of `file`, example: `read.arrow`, multiple_sep: `\";\"`. Input feather file(s), separated by \";\"." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "outdir": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.outdir`. Specify directory in which output has to be created", - "help_text": "Type: `file`, required, default: `$id.$key.outdir`. Specify directory in which output has to be created." - , - "default":"$id.$key.outdir" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write log messages also to terminal", - "help_text": "Type: `boolean_true`, default: `false`. Write log messages also to terminal" - , - "default":false - } - - - , - "store": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Store the extracted data in a pickle file for future plotting", - "help_text": "Type: `boolean_true`, default: `false`. Store the extracted data in a pickle file for future plotting." - , - "default":false - } - - - , - "raw": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Store the extracted data in tab separated file", - "help_text": "Type: `boolean_true`, default: `false`. Store the extracted data in tab separated file." - , - "default":false - } - - - , - "huge": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input data is one very large file", - "help_text": "Type: `boolean_true`, default: `false`. Input data is one very large file." - , - "default":false - } - - - , - "no_static": { - "type": - "boolean", - "description": "Type: `boolean_false`, default: `true`. Do not make static (png) plots", - "help_text": "Type: `boolean_false`, default: `true`. Do not make static (png) plots." - , - "default":true - } - - - , - "prefix": { - "type": - "string", - "description": "Type: `string`. Specify an optional prefix to be used for the output files", - "help_text": "Type: `string`. Specify an optional prefix to be used for the output files." - - } - - - , - "tsv_stats": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output the stats file as a properly formatted TSV", - "help_text": "Type: `boolean_true`, default: `false`. Output the stats file as a properly formatted TSV." - , - "default":false - } - - - , - "only_report": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output only the report", - "help_text": "Type: `boolean_true`, default: `false`. Output only the report." - , - "default":false - } - - - , - "info_in_report": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add NanoPlot run info in the report", - "help_text": "Type: `boolean_true`, default: `false`. Add NanoPlot run info in the report." - , - "default":false - } - - -} -}, - - - "filtering or transforming input" : { - "title": "Filtering or transforming input", - "type": "object", - "description": "No description", - "properties": { - - - "maxlength": { - "type": - "integer", - "description": "Type: `integer`. Drop reads longer than length specified", - "help_text": "Type: `integer`. Drop reads longer than length specified." - - } - - - , - "minlength": { - "type": - "integer", - "description": "Type: `integer`. Drop reads shorter than length specified", - "help_text": "Type: `integer`. Drop reads shorter than length specified." - - } - - - , - "drop_outliers": { - "type": - "boolean", - "description": "Type: `boolean_false`, default: `true`. Drop outlier reads with extreme long length", - "help_text": "Type: `boolean_false`, default: `true`. Drop outlier reads with extreme long length." - , - "default":true - } - - - , - "downsample": { - "type": - "integer", - "description": "Type: `integer`. Reduce dataset to N reads by random sampling", - "help_text": "Type: `integer`. Reduce dataset to N reads by random sampling." - - } - - - , - "loglength": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Logarithmic scaling of lengths in plots", - "help_text": "Type: `boolean_true`, default: `false`. Logarithmic scaling of lengths in plots." - , - "default":false - } - - - , - "percentqual": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use qualities as theoretical percent identities", - "help_text": "Type: `boolean_true`, default: `false`. Use qualities as theoretical percent identities." - , - "default":false - } - - - , - "alength": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use aligned read lengths rather than sequenced length (bam mode)", - "help_text": "Type: `boolean_true`, default: `false`. Use aligned read lengths rather than sequenced length (bam mode)." - , - "default":false - } - - - , - "minqual": { - "type": - "integer", - "description": "Type: `integer`. Drop reads with an average quality lower than specified", - "help_text": "Type: `integer`. Drop reads with an average quality lower than specified." - - } - - - , - "runtime_until": { - "type": - "integer", - "description": "Type: `integer`. Only take the N first hours of a run", - "help_text": "Type: `integer`. Only take the N first hours of a run." - - } - - - , - "readtype": { - "type": - "string", - "description": "Type: `string`. Which read type to extract information about from summary", - "help_text": "Type: `string`. Which read type to extract information about from summary.\nOptions are 1D, 2D, 1D2\n" - - } - - - , - "barcoded": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use if you want to split the summary file by barcode", - "help_text": "Type: `boolean_true`, default: `false`. Use if you want to split the summary file by barcode." - , - "default":false - } - - - , - "no_supplementary": { - "type": - "boolean", - "description": "Type: `boolean_false`, default: `true`. Use if you want to remove supplementary alignments", - "help_text": "Type: `boolean_false`, default: `true`. Use if you want to remove supplementary alignments." - , - "default":true - } - - -} -}, - - - "customizing plots" : { - "title": "Customizing plots", - "type": "object", - "description": "No description", - "properties": { - - - "color": { - "type": - "string", - "description": "Type: `string`. Specify a color for the plots, must be a valid matplotlib color", - "help_text": "Type: `string`. Specify a color for the plots, must be a valid matplotlib color." - - } - - - , - "colormap": { - "type": - "string", - "description": "Type: `string`. Specify a valid matplotlib colormap for the heatmap", - "help_text": "Type: `string`. Specify a valid matplotlib colormap for the heatmap." - - } - - - , - "format": { - "type": - "string", - "description": "Type: `string`, default: `png`. Specify the output format of the plots", - "help_text": "Type: `string`, default: `png`. Specify the output format of the plots.\n{eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}\n" - , - "default":"png" - } - - - , - "plots": { - "type": - "string", - "description": "Type: `string`. Specify which bivariate plots have to be made", - "help_text": "Type: `string`. Specify which bivariate plots have to be made.\n[{kde,hex,dot} ...]\n" - - } - - - , - "legacy": { - "type": - "string", - "description": "Type: `string`. Specify which bivariate plots have to be made (legacy mode)", - "help_text": "Type: `string`. Specify which bivariate plots have to be made (legacy mode).\n[{kde,dot,hex} ...]\n" - - } - - - , - "listcolors": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. List the colors which are available for plotting and exit", - "help_text": "Type: `boolean_true`, default: `false`. List the colors which are available for plotting and exit." - , - "default":false - } - - - , - "listcolormaps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. List the colormaps which are available for plotting and exit", - "help_text": "Type: `boolean_true`, default: `false`. List the colormaps which are available for plotting and exit." - , - "default":false - } - - - , - "no_N50": { - "type": - "boolean", - "description": "Type: `boolean_false`, default: `true`. Hide the N50 mark in the read length histogram", - "help_text": "Type: `boolean_false`, default: `true`. Hide the N50 mark in the read length histogram." - , - "default":true - } - - - , - "N50": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Show the N50 mark in the read length histogram", - "help_text": "Type: `boolean_true`, default: `false`. Show the N50 mark in the read length histogram." - , - "default":false - } - - - , - "title": { - "type": - "string", - "description": "Type: `string`. Add a title to all plots, requires quoting if using spaces", - "help_text": "Type: `string`. Add a title to all plots, requires quoting if using spaces." - - } - - - , - "font_scale": { - "type": - "number", - "description": "Type: `double`. Scale the font of the plots by a factor", - "help_text": "Type: `double`. Scale the font of the plots by a factor." - - } - - - , - "dpi": { - "type": - "integer", - "description": "Type: `integer`. Set the dpi for saving images", - "help_text": "Type: `integer`. Set the dpi for saving images." - - } - - - , - "hide_stats": { - "type": - "boolean", - "description": "Type: `boolean_false`, default: `true`. Not adding Pearson R stats in some bivariate plots", - "help_text": "Type: `boolean_false`, default: `true`. Not adding Pearson R stats in some bivariate plots." - , - "default":true - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "nanoplot", + "description": "Run NanoPlot on nanopore-sequenced reads.\nNanoPlot is a plotting tool for long read sequencing data and alignments.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "fastq": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fastq file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.fq\"]`. " + }, + "fasta": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fasta file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.fa\"]`. " + }, + "fastq_rich": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fastq file(s) generated by albacore or \nMinKNOW with additional information concerning channel and time, separated by \";\".\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.fq\"]`. " + }, + "fastq_minimal": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fastq file(s) generated by albacore or MinKNOW with\nadditional information concerning channel and time", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.fq\"]`. " + }, + "summary": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input summary file(s) generated by albacore or guppy, separated by \";\".\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.txt\"]`. " + }, + "bam": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input sorted bam file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.bam\"]`. " + }, + "ubam": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input unmapped bam file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.ubam\"]`. " + }, + "cram": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input sorted cram file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.cram\"]`. " + }, + "pickle": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input pickle file stored earlier, separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.pkl\"]`. " + }, + "feather": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input feather file(s), separated by \";\".", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"read.arrow\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "outdir": { + "type": "string", + "format": "path", + "description": "Specify directory in which output has to be created.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.outdir\"`, direction: `output`. ", + "default": "$id.$key.outdir" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "verbose": { + "type": "boolean", + "description": "Write log messages also to terminal", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "store": { + "type": "boolean", + "description": "Store the extracted data in a pickle file for future plotting.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "raw": { + "type": "boolean", + "description": "Store the extracted data in tab separated file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "huge": { + "type": "boolean", + "description": "Input data is one very large file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_static": { + "type": "boolean", + "description": "Do not make static (png) plots.", + "help_text": "Type: `boolean_false`, multiple: `False`, default: `true`. ", + "default": true + }, + "prefix": { + "type": "string", + "description": "Specify an optional prefix to be used for the output files.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "tsv_stats": { + "type": "boolean", + "description": "Output the stats file as a properly formatted TSV.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "only_report": { + "type": "boolean", + "description": "Output only the report.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "info_in_report": { + "type": "boolean", + "description": "Add NanoPlot run info in the report.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/filtering or transforming input" + "filtering or transforming input": { + "title": "Filtering or transforming input", + "type": "object", + "description": "No description", + "properties": { + "maxlength": { + "type": "integer", + "description": "Drop reads longer than length specified.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "minlength": { + "type": "integer", + "description": "Drop reads shorter than length specified.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "drop_outliers": { + "type": "boolean", + "description": "Drop outlier reads with extreme long length.", + "help_text": "Type: `boolean_false`, multiple: `False`, default: `true`. ", + "default": true + }, + "downsample": { + "type": "integer", + "description": "Reduce dataset to N reads by random sampling.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "loglength": { + "type": "boolean", + "description": "Logarithmic scaling of lengths in plots.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "percentqual": { + "type": "boolean", + "description": "Use qualities as theoretical percent identities.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "alength": { + "type": "boolean", + "description": "Use aligned read lengths rather than sequenced length (bam mode).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "minqual": { + "type": "integer", + "description": "Drop reads with an average quality lower than specified.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "runtime_until": { + "type": "integer", + "description": "Only take the N first hours of a run.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "readtype": { + "type": "string", + "description": "Which read type to extract information about from summary.\nOptions are 1D, 2D, 1D2\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "barcoded": { + "type": "boolean", + "description": "Use if you want to split the summary file by barcode.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_supplementary": { + "type": "boolean", + "description": "Use if you want to remove supplementary alignments.", + "help_text": "Type: `boolean_false`, multiple: `False`, default: `true`. ", + "default": true + } + } }, - - { - "$ref": "#/definitions/customizing plots" + "customizing plots": { + "title": "Customizing plots", + "type": "object", + "description": "No description", + "properties": { + "color": { + "type": "string", + "description": "Specify a color for the plots, must be a valid matplotlib color.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "colormap": { + "type": "string", + "description": "Specify a valid matplotlib colormap for the heatmap.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "format": { + "type": "string", + "description": "Specify the output format of the plots.\n{eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}\n", + "help_text": "Type: `string`, multiple: `False`, default: `\"png\"`. ", + "default": "png" + }, + "plots": { + "type": "string", + "description": "Specify which bivariate plots have to be made.\n[{kde,hex,dot} ...]\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "legacy": { + "type": "string", + "description": "Specify which bivariate plots have to be made (legacy mode).\n[{kde,dot,hex} ...]\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "listcolors": { + "type": "boolean", + "description": "List the colors which are available for plotting and exit.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "listcolormaps": { + "type": "boolean", + "description": "List the colormaps which are available for plotting and exit.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_N50": { + "type": "boolean", + "description": "Hide the N50 mark in the read length histogram.", + "help_text": "Type: `boolean_false`, multiple: `False`, default: `true`. ", + "default": true + }, + "N50": { + "type": "boolean", + "description": "Show the N50 mark in the read length histogram.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "title": { + "type": "string", + "description": "Add a title to all plots, requires quoting if using spaces.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "font_scale": { + "type": "number", + "description": "Scale the font of the plots by a factor.", + "help_text": "Type: `double`, multiple: `False`. " + }, + "dpi": { + "type": "integer", + "description": "Set the dpi for saving images.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "hide_stats": { + "type": "boolean", + "description": "Not adding Pearson R stats in some bivariate plots.", + "help_text": "Type: `boolean_false`, multiple: `False`, default: `true`. ", + "default": true + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/filtering or transforming input" + }, + { + "$ref": "#/$defs/customizing plots" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 057f6e75..cb6c46f2 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -7,17 +7,9 @@ authors: - "maintainer" info: links: - email: "kai@data-intuitive.com" github: "KaiWaldrant" orcid: "0009-0003-8555-1361" linkedin: "kaiwaldrant" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" - - name: "Open Problems" - href: "https://openproblems.bio" - role: "Contributor" argument_groups: - name: "Inputs" arguments: @@ -401,9 +393,9 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -428,6 +420,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index c79484ce..23a8848b 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3044,23 +3044,10 @@ meta = [ ], "info" : { "links" : { - "email" : "kai@data-intuitive.com", "github" : "KaiWaldrant", "orcid" : "0009-0003-8555-1361", "linkedin" : "kaiwaldrant" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - }, - { - "name" : "Open Problems", - "href" : "https://openproblems.bio", - "role" : "Contributor" - } - ] + } } } ], @@ -3489,9 +3476,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3507,6 +3494,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/pear/nextflow_schema.json b/target/nextflow/pear/nextflow_schema.json index d5245704..a46d763c 100644 --- a/target/nextflow/pear/nextflow_schema.json +++ b/target/nextflow/pear/nextflow_schema.json @@ -1,284 +1,164 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "pear", -"description": "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.\n\nPEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "forward_fastq": { - "type": - "string", - "description": "Type: `file`, required, example: `forward.fastq`. Forward paired-end FASTQ file", - "help_text": "Type: `file`, required, example: `forward.fastq`. Forward paired-end FASTQ file" - - } - - - , - "reverse_fastq": { - "type": - "string", - "description": "Type: `file`, required, example: `reverse.fastq`. Reverse paired-end FASTQ file", - "help_text": "Type: `file`, required, example: `reverse.fastq`. Reverse paired-end FASTQ file" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "assembled": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.assembled`. The output file containing assembled reads", - "help_text": "Type: `file`, required, default: `$id.$key.assembled`. The output file containing assembled reads. Can be compressed with gzip." - , - "default":"$id.$key.assembled" - } - - - , - "unassembled_forward": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.unassembled_forward`. The output file containing forward reads that could not be assembled", - "help_text": "Type: `file`, required, default: `$id.$key.unassembled_forward`. The output file containing forward reads that could not be assembled. Can be compressed with gzip." - , - "default":"$id.$key.unassembled_forward" - } - - - , - "unassembled_reverse": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.unassembled_reverse`. The output file containing reverse reads that could not be assembled", - "help_text": "Type: `file`, required, default: `$id.$key.unassembled_reverse`. The output file containing reverse reads that could not be assembled. Can be compressed with gzip." - , - "default":"$id.$key.unassembled_reverse" - } - - - , - "discarded": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases", - "help_text": "Type: `file`, required, default: `$id.$key.discarded`. The output file containing reads that were discarded due to too low quality or too many uncalled bases. Can be compressed with gzip." - , - "default":"$id.$key.discarded" - } - - -} -}, - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "p_value": { - "type": - "number", - "description": "Type: `double`, example: `0.01`. Specify a p-value for the statistical test", - "help_text": "Type: `double`, example: `0.01`. Specify a p-value for the statistical test. If the computed p-value of a possible assembly exceeds the specified p-value then paired-end read will not be assembled. Valid options are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables the test.\n" - - } - - - , - "min_overlap": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. Specify the minimum overlap size", - "help_text": "Type: `integer`, example: `10`. Specify the minimum overlap size. The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles.\n" - - } - - - , - "max_assembly_length": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Specify the maximum possible length of the assembled sequences", - "help_text": "Type: `integer`, example: `0`. Specify the maximum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long.\n" - - } - - - , - "min_assembly_length": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Specify the minimum possible length of the assembled sequences", - "help_text": "Type: `integer`, example: `0`. Specify the minimum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short.\n" - - } - - - , - "min_trim_length": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Specify the minimum length of reads after trimming the low quality part (see option -q)\n", - "help_text": "Type: `integer`, example: `1`. Specify the minimum length of reads after trimming the low quality part (see option -q)\n" - - } - - - , - "quality_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Specify the quality threshold for trimming the low quality part of a read", - "help_text": "Type: `integer`, example: `0`. Specify the quality threshold for trimming the low quality part of a read. If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed.\n" - - } - - - , - "max_uncalled_base": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. Specify the maximal proportion of uncalled bases in a read", - "help_text": "Type: `double`, example: `1.0`. Specify the maximal proportion of uncalled bases in a read. Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases.\n" - - } - - - , - "test_method": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Specify the type of statistical test", - "help_text": "Type: `integer`, example: `1`. Specify the type of statistical test. Two options are available. 1: Given the minimum allowed overlap, test using the highest OES. Note that due to its discrete nature, this test usually yields a lower p-value for the assembled read than the cut- off (specified by -p). For example, setting the cut-off to 0.05 using this test, the assembled reads might have an actual p-value of 0.02.\n2. Use the acceptance probability (m.a.p). This test methods computes the same probability as test method 1. However, it assumes that the minimal overlap is the observed overlap with the highest OES, instead of the one specified by -v. Therefore, this is not a valid statistical test and the \u0027p-value\u0027 is in fact the maximal probability for accepting the assembly. Nevertheless, we observed in practice that for the case the actual overlap sizes are relatively small, test 2 can correctly assemble more reads with only slightly higher false-positive rate.\n" - - } - - - , - "emperical_freqs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable empirical base frequencies", - "help_text": "Type: `boolean_true`, default: `false`. Disable empirical base frequencies.\n" - , - "default":false - } - - - , - "score_method": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. Specify the scoring method", - "help_text": "Type: `integer`, example: `2`. Specify the scoring method. 1. OES with +1 for match and -1 for mismatch. 2: Assembly score (AS). Use +1 for match and -1 for mismatch multiplied by base quality scores. 3: Ignore quality scores and use +1 for a match and -1 for a mismatch.\n" - - } - - - , - "phred_base": { - "type": - "integer", - "description": "Type: `integer`, example: `33`. Base PHRED quality score", - "help_text": "Type: `integer`, example: `33`. Base PHRED quality score.\n" - - } - - - , - "cap": { - "type": - "integer", - "description": "Type: `integer`, example: `40`. Specify the upper bound for the resulting quality score", - "help_text": "Type: `integer`, example: `40`. Specify the upper bound for the resulting quality score. If set to zero, capping is disabled.\n" - - } - - - , - "nbase": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases\n", - "help_text": "Type: `boolean_true`, default: `false`. When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "pear", + "description": "PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.\n\nPEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "forward_fastq": { + "type": "string", + "format": "path", + "exists": true, + "description": "Forward paired-end FASTQ file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"forward.fastq\"`. " + }, + "reverse_fastq": { + "type": "string", + "format": "path", + "exists": true, + "description": "Reverse paired-end FASTQ file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"reverse.fastq\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "assembled": { + "type": "string", + "format": "path", + "description": "The output file containing assembled reads", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.assembled\"`, direction: `output`. ", + "default": "$id.$key.assembled" + }, + "unassembled_forward": { + "type": "string", + "format": "path", + "description": "The output file containing forward reads that could not be assembled", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.unassembled_forward\"`, direction: `output`. ", + "default": "$id.$key.unassembled_forward" + }, + "unassembled_reverse": { + "type": "string", + "format": "path", + "description": "The output file containing reverse reads that could not be assembled", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.unassembled_reverse\"`, direction: `output`. ", + "default": "$id.$key.unassembled_reverse" + }, + "discarded": { + "type": "string", + "format": "path", + "description": "The output file containing reads that were discarded due to too low quality or too many uncalled bases", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.discarded\"`, direction: `output`. ", + "default": "$id.$key.discarded" + } + } }, - - { - "$ref": "#/definitions/arguments" + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "p_value": { + "type": "number", + "description": "Specify a p-value for the statistical test", + "help_text": "Type: `double`, multiple: `False`, example: `0.01`. " + }, + "min_overlap": { + "type": "integer", + "description": "Specify the minimum overlap size", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "max_assembly_length": { + "type": "integer", + "description": "Specify the maximum possible length of the assembled sequences", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "min_assembly_length": { + "type": "integer", + "description": "Specify the minimum possible length of the assembled sequences", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "min_trim_length": { + "type": "integer", + "description": "Specify the minimum length of reads after trimming the low quality part (see option -q)\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "quality_threshold": { + "type": "integer", + "description": "Specify the quality threshold for trimming the low quality part of a read", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "max_uncalled_base": { + "type": "number", + "description": "Specify the maximal proportion of uncalled bases in a read", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + }, + "test_method": { + "type": "integer", + "description": "Specify the type of statistical test", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "emperical_freqs": { + "type": "boolean", + "description": "Disable empirical base frequencies.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "score_method": { + "type": "integer", + "description": "Specify the scoring method", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "phred_base": { + "type": "integer", + "description": "Base PHRED quality score.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `33`. " + }, + "cap": { + "type": "integer", + "description": "Specify the upper bound for the resulting quality score", + "help_text": "Type: `integer`, multiple: `False`, example: `40`. " + }, + "nbase": { + "type": "boolean", + "description": "When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index 9535cfc2..9b78ae6a 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -267,9 +267,9 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -294,6 +294,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index 24e3be33..fa35ca26 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -3359,9 +3359,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3377,6 +3377,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json index 47e34c91..bed9c38c 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json @@ -1,217 +1,136 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "qualimap_rnaseq", -"description": "Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5\u2019-3\u2019 bias computation.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "bam": { - "type": - "string", - "description": "Type: `file`, required, example: `alignment.bam`. Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner", - "help_text": "Type: `file`, required, example: `alignment.bam`. Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner." - - } - - - , - "gtf": { - "type": - "string", - "description": "Type: `file`, required, example: `annotations.gtf`. Path to genomic annotations in Ensembl GTF format", - "help_text": "Type: `file`, required, example: `annotations.gtf`. Path to genomic annotations in Ensembl GTF format." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "qc_results": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results", - "help_text": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results." - , - "default":"$id.$key.qc_results.txt" - } - - - , - "counts": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts", - "help_text": "Type: `file`, default: `$id.$key.counts`. Output file for computed counts." - , - "default":"$id.$key.counts" - } - - - , - "report": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file", - "help_text": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file. Supported formats are PDF or HTML." - , - "default":"$id.$key.report.html" - } - - -} -}, - - - "optional" : { - "title": "Optional", - "type": "object", - "description": "No description", - "properties": { - - - "num_pr_bases": { - "type": - "integer", - "description": "Type: `integer`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)", - "help_text": "Type: `integer`. Number of upstream/downstream nucleotide bases to compute 5\u0027-3\u0027 bias (default = 100)." - - } - - - , - "num_tr_bias": { - "type": - "integer", - "description": "Type: `integer`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)", - "help_text": "Type: `integer`. Number of top highly expressed transcripts to compute 5\u0027-3\u0027 bias (default = 1000)." - - } - - - , - "algorithm": { - "type": - "string", - "description": "Type: `string`, choices: ``uniquely-mapped-reads`, `proportional``. Counting algorithm (uniquely-mapped-reads (default) or proportional)", - "help_text": "Type: `string`, choices: ``uniquely-mapped-reads`, `proportional``. Counting algorithm (uniquely-mapped-reads (default) or proportional).", - "enum": ["uniquely-mapped-reads", "proportional"] - - - } - - - , - "sequencing_protocol": { - "type": - "string", - "description": "Type: `string`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default))", - "help_text": "Type: `string`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).", - "enum": ["non-strand-specific", "strand-specific-reverse", "strand-specific-forward"] - - - } - - - , - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads", - "help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads." - , - "default":false - } - - - , - "sorted": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name", - "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis." - , - "default":false - } - - - , - "java_memory_size": { - "type": - "string", - "description": "Type: `string`. maximum Java heap memory size, default = 4G", - "help_text": "Type: `string`. maximum Java heap memory size, default = 4G." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "qualimap_rnaseq", + "description": "Qualimap RNA-seq QC reports quality control metrics and bias estimations \nwhich are specific for whole transcriptome sequencing, including reads genomic \norigin, junction analysis, transcript coverage and 5’-3’ bias computation.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "bam": { + "type": "string", + "format": "path", + "exists": true, + "description": "Path to the sequence alignment file in BAM format, produced by a splicing-aware aligner.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"alignment.bam\"`. " + }, + "gtf": { + "type": "string", + "format": "path", + "exists": true, + "description": "Path to genomic annotations in Ensembl GTF format.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"annotations.gtf\"`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "qc_results": { + "type": "string", + "format": "path", + "description": "Text file containing the RNAseq QC results.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.qc_results.txt\"`, direction: `output`, example: `\"rnaseq_qc_results.txt\"`. ", + "default": "$id.$key.qc_results.txt" + }, + "counts": { + "type": "string", + "format": "path", + "description": "Output file for computed counts.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.counts\"`, direction: `output`. ", + "default": "$id.$key.counts" + }, + "report": { + "type": "string", + "format": "path", + "description": "Report output file", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.report.html\"`, direction: `output`, example: `\"report.html\"`. ", + "default": "$id.$key.report.html" + } + } }, - - { - "$ref": "#/definitions/optional" + "optional": { + "title": "Optional", + "type": "object", + "description": "No description", + "properties": { + "num_pr_bases": { + "type": "integer", + "description": "Number of upstream/downstream nucleotide bases to compute 5'-3' bias (default = 100).", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "num_tr_bias": { + "type": "integer", + "description": "Number of top highly expressed transcripts to compute 5'-3' bias (default = 1000).", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "algorithm": { + "type": "string", + "description": "Counting algorithm (uniquely-mapped-reads (default) or proportional).", + "help_text": "Type: `string`, multiple: `False`, choices: ``uniquely-mapped-reads`, `proportional``. ", + "enum": [ + "uniquely-mapped-reads", + "proportional" + ] + }, + "sequencing_protocol": { + "type": "string", + "description": "Sequencing library protocol (strand-specific-forward, strand-specific-reverse or non-strand-specific (default)).", + "help_text": "Type: `string`, multiple: `False`, choices: ``non-strand-specific`, `strand-specific-reverse`, `strand-specific-forward``. ", + "enum": [ + "non-strand-specific", + "strand-specific-reverse", + "strand-specific-forward" + ] + }, + "paired": { + "type": "boolean", + "description": "Setting this flag for paired-end experiments will result in counting fragments instead of reads.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sorted": { + "type": "boolean", + "description": "Setting this flag indicates that the input file is already sorted by name", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "java_memory_size": { + "type": "string", + "description": "maximum Java heap memory size, default = 4G.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/optional" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 990e5f0e..1a6ed96a 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -855,9 +855,9 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -882,6 +882,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index ef7713b4..41dbebc9 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3891,9 +3891,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3909,6 +3909,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json index 63db46df..8d5631c9 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json @@ -1,839 +1,488 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rsem_calculate_expression", -"description": "Calculate expression with RSEM. \n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "id": { - "type": - "string", - "description": "Type: `string`. Sample ID", - "help_text": "Type: `string`. Sample ID." - - } - - - , - "strandedness": { - "type": - "string", - "description": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. Sample strand-specificity", - "help_text": "Type: `string`, choices: ``forward`, `reverse`, `unstranded``. Sample strand-specificity. Must be one of unstranded, forward, reverse", - "enum": ["forward", "reverse", "unstranded"] - - - } - - - , - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Paired-end reads or not?", - "help_text": "Type: `boolean_true`, default: `false`. Paired-end reads or not?" - , - "default":false - } - - - , - "input": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Input reads for quantification", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Input reads for quantification." - - } - - - , - "index": { - "type": - "string", - "description": "Type: `file`. RSEM index", - "help_text": "Type: `file`. RSEM index." - - } - - - , - "extra_args": { - "type": - "string", - "description": "Type: `string`. Extra rsem-calculate-expression arguments in addition to the examples", - "help_text": "Type: `string`. Extra rsem-calculate-expression arguments in addition to the examples." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "counts_gene": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level", - "help_text": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level" - , - "default":"$id.$key.counts_gene.results" - } - - - , - "counts_transcripts": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level", - "help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level" - , - "default":"$id.$key.counts_transcripts.results" - } - - - , - "stat": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics", - "help_text": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics" - , - "default":"$id.$key.stat.stat" - } - - - , - "logs": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs", - "help_text": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs" - , - "default":"$id.$key.logs.log" - } - - - , - "bam_star": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)", - "help_text": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)" - , - "default":"$id.$key.bam_star.bam" - } - - - , - "bam_genome": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)", - "help_text": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)" - , - "default":"$id.$key.bam_genome.bam" - } - - - , - "bam_transcript": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)", - "help_text": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)" - , - "default":"$id.$key.bam_transcript.bam" - } - - - , - "sort_bam_by_read_name": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name", - "help_text": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce \ndeterministic maximum likelihood estimations from independent runs. Note that sorting will take long \ntime and lots of memory.\n" - , - "default":false - } - - - , - "no_bam_output": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not output any BAM file", - "help_text": "Type: `boolean_true`, default: `false`. Do not output any BAM file." - , - "default":false - } - - - , - "sampling_for_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities", - "help_text": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure \nincludes the alignment to the \"noise\" transcript, which does not appear in the BAM file. Only the \nsampled alignment has a weight of 1. All other alignments have weight 0. If the \"noise\" transcript is \nsampled, all alignments appeared in the BAM file should have weight 0.\n" - , - "default":false - } - - - , - "output_genome_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name", - "help_text": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name.genome.bam\u0027, with alignments mapped to genomic coordinates and \nannotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM \npackage) to sort and index the bam file. \u0027sample_name.genome.sorted.bam\u0027 and \u0027sample_name.genome.sorted.bam.bai\u0027 \nwill be generated.\n" - , - "default":false - } - - - , - "sort_bam_by_coordinate": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices", - "help_text": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.\n" - , - "default":false - } - - -} -}, - - - "basic options" : { - "title": "Basic Options", - "type": "object", - "description": "No description", - "properties": { - - - "no_qualities": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores", - "help_text": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores." - , - "default":false - } - - - , - "alignments": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format", - "help_text": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format. The exact file format will be determined \nautomatically.\n" - , - "default":false - } - - - , - "fai": { - "type": - "string", - "description": "Type: `file`. If the header section of input alignment file does not contain reference sequence information, \nthis option should be turned on", - "help_text": "Type: `file`. If the header section of input alignment file does not contain reference sequence information, \nthis option should be turned on. \u003cfile\u003e is a FAI format file containing each reference sequence\u0027s \nname and length. Please refer to the SAM official website for the details of FAI format.\n" - - } - - - , - "bowtie2": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads", - "help_text": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local \nand discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In \nparticular, we use options \u0027--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score_min L,0,-0.1\u0027 \nby default. The last parameter of \u0027--score_min\u0027, \u0027-0.1\u0027, is the negative of maximum mismatch rate. \nThis rate can be set by option \u0027--bowtie2_mismatch_rate\u0027. If reads are paired-end, we additionally \nuse options \u0027--no_mixed\u0027 and \u0027--no_discordant\u0027.\n" - , - "default":false - } - - - , - "star": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use STAR to align reads", - "help_text": "Type: `boolean_true`, default: `false`. Use STAR to align reads. Alignment parameters are from ENCODE3\u0027s STAR-RSEM pipeline. To save \ncomputational time and memory resources, STAR\u0027s Output BAM file is unsorted. It is stored in RSEM\u0027s \ntemporary directory with name as \u0027sample_name.bam\u0027. Each STAR job will have its own private copy of \nthe genome in memory.\n" - , - "default":false - } - - - , - "hisat2_hca": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast", - "help_text": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.\n" - , - "default":false - } - - - , - "append_names": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name", - "help_text": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name.isoforms.results\u0027 and \u0027sample_name.genes.results\u0027.\n" - , - "default":false - } - - - , - "seed": { - "type": - "integer", - "description": "Type: `integer`. Set the seed for the random number generators used in calculating posterior mean estimates and \ncredibility intervals", - "help_text": "Type: `integer`. Set the seed for the random number generators used in calculating posterior mean estimates and \ncredibility intervals. The seed must be a non-negative 32 bit integer.\n" - - } - - - , - "single_cell_prior": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals", - "help_text": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals. However, much less genes are expressed in single cell RNA-Seq data. Thus, if you want to \ncompute posterior mean estimates and/or credibility intervals and you have single-cell RNA-Seq data, \nyou are recommended to turn on this option. Then RSEM will use Dirichlet(0.1) as the prior which \nencourage the sparsity of the expression levels.\n" - , - "default":false - } - - - , - "calc_pme": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates", - "help_text": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates." - , - "default":false - } - - - , - "calc_ci": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates", - "help_text": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates. The credibility level can be \nchanged by setting \u0027--ci_credibility_level\u0027.\n" - , - "default":false - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information", - "help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information." - , - "default":false - } - - -} -}, - - - "aligner options" : { - "title": "Aligner Options", - "type": "object", - "description": "No description", - "properties": { - - - "seed_length": { - "type": - "integer", - "description": "Type: `integer`, example: `25`. Seed length used by the read aligner", - "help_text": "Type: `integer`, example: `25`. Seed length used by the read aligner. Providing the correct value is important for RSEM. If RSEM \nruns Bowtie, it uses this value for Bowtie\u0027s seed length parameter. Any read with its or at least \none of its mates\u0027 (for paired-end reads) length less than this value will be ignored. If the \nreferences are not added poly(A) tails, the minimum allowed value is 5, otherwise, the minimum \nallowed value is 25. Note that this script will only check if the value \u003e= 5 and give a warning \nmessage if the value \u003c 25 but \u003e= 5. (Default: 25)\n" - - } - - - , - "phred64_quals": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver", - "help_text": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. \u003e= 1.3). This option is \nused by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n" - , - "default":false - } - - - , - "solexa_quals": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver", - "help_text": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver. \u003c 1.3). This option is used by \nBowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n" - , - "default":false - } - - - , - "bowtie_n": { - "type": - "integer", - "description": "Type: `integer`, example: `2`, choices: ``0`, `1`, `2`, `3``. (Bowtie parameter) max # of mismatches in the seed", - "help_text": "Type: `integer`, example: `2`, choices: ``0`, `1`, `2`, `3``. (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3, Default: 2)\n", - "enum": [0, 1, 2, 3] - - - } - - - , - "bowtie_e": { - "type": - "integer", - "description": "Type: `integer`, example: `99999999`. (Bowtie parameter) max sum of mismatch quality scores across the alignment", - "help_text": "Type: `integer`, example: `99999999`. (Bowtie parameter) max sum of mismatch quality scores across the alignment. (Default: 99999999)\n" - - } - - - , - "bowtie_m": { - "type": - "integer", - "description": "Type: `integer`, example: `200`. (Bowtie parameter) suppress all alignments for a read if \u003e \u003cint\u003e valid alignments exist", - "help_text": "Type: `integer`, example: `200`. (Bowtie parameter) suppress all alignments for a read if \u003e \u003cint\u003e valid alignments exist. (Default: 200)\n" - - } - - - , - "bowtie_chunkmbs": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. (Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use Bowtie\u0027s default)\n", - "help_text": "Type: `integer`, example: `0`. (Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use Bowtie\u0027s default)\n" - - } - - - , - "bowtie2_mismatch_rate": { - "type": - "number", - "description": "Type: `double`, example: `0.1`. (Bowtie 2 parameter) The maximum mismatch rate allowed", - "help_text": "Type: `double`, example: `0.1`. (Bowtie 2 parameter) The maximum mismatch rate allowed. (Default: 0.1)\n" - - } - - - , - "bowtie2_k": { - "type": - "integer", - "description": "Type: `integer`, example: `200`. (Bowtie 2 parameter) Find up to \u003cint\u003e alignments per read", - "help_text": "Type: `integer`, example: `200`. (Bowtie 2 parameter) Find up to \u003cint\u003e alignments per read. (Default: 200)\n" - - } - - - , - "bowtie2_sensitivity_level": { - "type": - "string", - "description": "Type: `string`, example: `sensitive`, choices: ``very_fast`, `fast`, `sensitive`, `very_sensitive``. (Bowtie 2 parameter) Set Bowtie 2\u0027s preset options in --end-to-end mode", - "help_text": "Type: `string`, example: `sensitive`, choices: ``very_fast`, `fast`, `sensitive`, `very_sensitive``. (Bowtie 2 parameter) Set Bowtie 2\u0027s preset options in --end-to-end mode. This option controls how \nhard Bowtie 2 tries to find alignments. \u003cstring\u003e must be one of \"very_fast\", \"fast\", \"sensitive\" \nand \"very_sensitive\". The four candidates correspond to Bowtie 2\u0027s \"--very-fast\", \"--fast\", \n\"--sensitive\" and \"--very-sensitive\" options. (Default: \"sensitive\" - use Bowtie 2\u0027s default)\n", - "enum": ["very_fast", "fast", "sensitive", "very_sensitive"] - - - } - - - , - "star_gzipped_read_file": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip", - "help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip. (Default: false)\n" - , - "default":false - } - - - , - "star_bzipped_read_file": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2", - "help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2. (Default: false)\n" - , - "default":false - } - - - , - "star_output_genome_bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name", - "help_text": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name.STAR.genome.bam\u0027. \nThis file is NOT sorted by genomic coordinate. In this file, according to STAR\u0027s manual, \u0027paired \nends of an alignment are always adjacent, and multiple alignments of a read are adjacent as well\u0027. \n(Default: false)\n" - , - "default":false - } - - -} -}, - - - "advanced options" : { - "title": "Advanced Options", - "type": "object", - "description": "No description", - "properties": { - - - "tag": { - "type": - "string", - "description": "Type: `string`, example: ``. The name of the optional field used in the SAM input for identifying a read with too many valid \nalignments", - "help_text": "Type: `string`, example: ``. The name of the optional field used in the SAM input for identifying a read with too many valid \nalignments. The field should have the format \u003ctagName\u003e:i:\u003cvalue\u003e, where a \u003cvalue\u003e bigger than 0 \nindicates a read with too many alignments. (Default: \"\")\n" - - } - - - , - "fragment_length_min": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Minimum read/insert length allowed", - "help_text": "Type: `integer`, example: `1`. Minimum read/insert length allowed. This is also the value for the Bowtie/Bowtie2 -I option. \n(Default: 1)\n" - - } - - - , - "fragment_length_max": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. Maximum read/insert length allowed", - "help_text": "Type: `integer`, example: `1000`. Maximum read/insert length allowed. This is also the value for the Bowtie/Bowtie 2 -X option. \n(Default: 1000)\n" - - } - - - , - "fragment_length_mean": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. (single-end data only) The mean of the fragment length distribution, which is assumed to be a \nGaussian", - "help_text": "Type: `integer`, example: `-1`. (single-end data only) The mean of the fragment length distribution, which is assumed to be a \nGaussian. (Default: -1, which disables use of the fragment length distribution)\n" - - } - - - , - "gragment_length_sd": { - "type": - "number", - "description": "Type: `double`, example: `0.0`. (single-end data only) The standard deviation of the fragment length distribution, which is \nassumed to be a Gaussian", - "help_text": "Type: `double`, example: `0.0`. (single-end data only) The standard deviation of the fragment length distribution, which is \nassumed to be a Gaussian. (Default: 0, which assumes that all fragments are of the same length, \ngiven by the rounded value of --fragment_length_mean).\n" - - } - - - , - "estimate_rspd": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data", - "help_text": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data.\nOtherwise, RSEM will use a uniform RSPD.\n" - , - "default":false - } - - - , - "num_rspd_bins": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. Number of bins in the RSPD", - "help_text": "Type: `integer`, example: `20`. Number of bins in the RSPD. Only relevant when \u0027--estimate_rspd\u0027 is specified. Use of the default \nsetting is recommended. (Default: 20)\n" - - } - - - , - "gibbs_burnin": { - "type": - "integer", - "description": "Type: `integer`, example: `200`. The number of burn-in rounds for RSEM\u0027s Gibbs sampler", - "help_text": "Type: `integer`, example: `200`. The number of burn-in rounds for RSEM\u0027s Gibbs sampler. Each round passes over the entire data set \nonce. If RSEM can use multiple threads, multiple Gibbs samplers will start at the same time and all \nsamplers share the same burn-in number. (Default: 200)\n" - - } - - - , - "gibbs_number_of_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. The total number of count vectors RSEM will collect from its Gibbs samplers", - "help_text": "Type: `integer`, example: `1000`. The total number of count vectors RSEM will collect from its Gibbs samplers. (Default: 1000)\n" - - } - - - , - "gibbs_sampling_gap": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. The number of rounds between two succinct count vectors RSEM collects", - "help_text": "Type: `integer`, example: `1`. The number of rounds between two succinct count vectors RSEM collects. If the count vector after \nround N is collected, the count vector after round N + \u003cint\u003e will also be collected. (Default: 1)\n" - - } - - - , - "ci_credibility_level": { - "type": - "number", - "description": "Type: `double`, example: `0.95`. The credibility level for credibility intervals", - "help_text": "Type: `double`, example: `0.95`. The credibility level for credibility intervals. (Default: 0.95)\n" - - } - - - , - "ci_number_of_samples_per_count_vector": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. The number of read generating probability vectors sampled per sampled count vector", - "help_text": "Type: `integer`, example: `50`. The number of read generating probability vectors sampled per sampled count vector. The crebility \nintervals are calculated by first sampling P(C | D) and then sampling P(Theta | C) for each sampled \ncount vector. This option controls how many Theta vectors are sampled per sampled count vector. \n(Default: 50)\n" - - } - - - , - "keep_intermediate_files": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM", - "help_text": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM. RSEM creates a temporary directory, \u0027sample_name.temp\u0027, \ninto which it puts all intermediate output files. If this directory already exists, RSEM overwrites \nall files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the \ntemporary directory is deleted. Set this option to prevent the deletion of this directory and the \nintermediate files inside of it.\n" - , - "default":false - } - - - , - "temporary_folder": { - "type": - "string", - "description": "Type: `string`, example: `sample_name.temp`. Set where to put the temporary files generated by RSEM", - "help_text": "Type: `string`, example: `sample_name.temp`. Set where to put the temporary files generated by RSEM. If the folder specified does not exist, \nRSEM will try to create it. (Default: sample_name.temp)\n" - - } - - - , - "time": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name", - "help_text": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name.time\u0027.\n" - , - "default":false - } - - -} -}, - - - "prior-enhanced rsem options" : { - "title": "Prior-Enhanced RSEM Options", - "type": "object", - "description": "No description", - "properties": { - - - "run_pRSEM": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM)", - "help_text": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e. isoform\u0027s initial pseudo-count for \nRSEM\u0027s Gibbs sampling, will be learned from input RNA-seq data and an external data set. When pRSEM \nneeds and only needs ChIP-seq peak information to partition isoforms (e.g. in pRSEM\u0027s default \npartition model), either ChIP-seq peak file (with the \u0027--chipseq_peak_file\u0027 option) or ChIP-seq \nFASTQ files for target and input and the path for Bowtie executables are required (with the \n\u0027--chipseq_target_read_files \u003cstring\u003e\u0027, \u0027--chipseq_control_read_files \u003cstring\u003e\u0027, and \u0027--bowtie_path \n\u003cpath\u003e options), otherwise, ChIP-seq FASTQ files for target and control and the path to Bowtie \nexecutables are required.\n" - , - "default":false - } - - - , - "chipseq_peak_file": { - "type": - "string", - "description": "Type: `file`. Full path to a ChIP-seq peak file in ENCODE\u0027s narrowPeak, i", - "help_text": "Type: `file`. Full path to a ChIP-seq peak file in ENCODE\u0027s narrowPeak, i.e. BED6+4, format. This file is used \nwhen running prior-enhanced RSEM in the default two-partition model. It partitions isoforms by \nwhether they have ChIP-seq overlapping with their transcription start site region or not. Each \npartition will have its own prior parameter learned from a training set. This file can be either \ngzipped or ungzipped.\n" - - } - - - , - "chipseq_target_read_files": { - "type": - "string", - "description": "Type: `file`. Comma-separated full path of FASTQ read file(s) for ChIP-seq target", - "help_text": "Type: `file`. Comma-separated full path of FASTQ read file(s) for ChIP-seq target. This option is used when running \nprior-enhanced RSEM. It provides information to calculate ChIP-seq peaks and signals. The file(s) \ncan be either ungzipped or gzipped with a suffix \u0027.gz\u0027 or \u0027.gzip\u0027. The options \u0027--bowtie_path \u003cpath\u003e\u0027 \nand \u0027--chipseq_control_read_files \u003cstring\u003e\u0027 must be defined when this option is specified.\n" - - } - - - , - "chipseq_control_read_files": { - "type": - "string", - "description": "Type: `file`. Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol", - "help_text": "Type: `file`. Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol. This option is used when running \nprior-enhanced RSEM. It provides information to call ChIP-seq peaks. The file(s) can be either \nungzipped or gzipped with a suffix \u0027.gz\u0027 or \u0027.gzip\u0027. The options \u0027--bowtie_path \u003cpath\u003e\u0027 and \n\u0027--chipseq_target_read_files \u003cstring\u003e\u0027 must be defined when this option is specified.\n" - - } - - - , - "chipseq_read_files_multi_targets": { - "type": - "string", - "description": "Type: `file`. Comma-separated full path of FASTQ read files for multiple ChIP-seq targets", - "help_text": "Type: `file`. Comma-separated full path of FASTQ read files for multiple ChIP-seq targets. This option is used when \nrunning prior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides \ninformation to calculate ChIP-seq signals. All files can be either ungzipped or gzipped with a suffix \n\u0027.gz\u0027 or \u0027.gzip\u0027. When this option is specified, the option \u0027--bowtie_path \u003cpath\u003e\u0027 must be defined and \nthe option \u0027--partition_model \u003cstring\u003e\u0027 will be set to \u0027cmb_lgt\u0027 automatically.\n" - - } - - - , - "chipseq_bed_files_multi_targets": { - "type": - "string", - "description": "Type: `file`. Comma-separated full path of BED files for multiple ChIP-seq targets", - "help_text": "Type: `file`. Comma-separated full path of BED files for multiple ChIP-seq targets. This option is used when running \nprior-enhanced RSEM, where prior is learned from multiple complementary data sets. It provides information \nof ChIP-seq signals and must have at least the first six BED columns. All files can be either ungzipped \nor gzipped with a suffix \u0027.gz\u0027 or \u0027.gzip\u0027. When this option is specified, the option \u0027--partition_model \n\u003cstring\u003e\u0027 will be set to \u0027cmb_lgt\u0027 automatically.\n" - - } - - - , - "cap_stacked_chipseq_reads": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval", - "help_text": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval. This option is used \nwhen running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This \noption is only in use when either \u0027--chipseq_read_files_multi_targets \u003cstring\u003e\u0027 or \n\u0027--chipseq_bed_files_multi_targets \u003cstring\u003e\u0027 is specified.\n" - , - "default":false - } - - - , - "n_max_stacked_chipseq_reads": { - "type": - "integer", - "description": "Type: `integer`. The maximum number of stacked ChIP-seq reads to keep", - "help_text": "Type: `integer`. The maximum number of stacked ChIP-seq reads to keep. This option is used when running prior-enhanced \nRSEM, where prior is learned from multiple complementary data sets. This option is only in use when the \noption \u0027--cap_stacked_chipseq_reads\u0027 is set.\n" - - } - - - , - "partition_model": { - "type": - "string", - "description": "Type: `string`, example: `pk`. A keyword to specify the partition model used by prior-enhanced RSEM", - "help_text": "Type: `string`, example: `pk`. A keyword to specify the partition model used by prior-enhanced RSEM. It must be one of the following \nkeywords:\n* pk\n* pk_lgtnopk\n* lm3, lm4, lm5, or lm6\n* nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk\n* pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk\n* cmb_lgt\nParameters for all the above models are learned from a training set. For detailed explanations, please \nsee prior-enhanced RSEM\u0027s paper. (Default: \u0027pk\u0027)\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "rsem_calculate_expression", + "description": "Calculate expression with RSEM. \n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "id": { + "type": "string", + "description": "Sample ID.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "strandedness": { + "type": "string", + "description": "Sample strand-specificity", + "help_text": "Type: `string`, multiple: `False`, choices: ``forward`, `reverse`, `unstranded``. ", + "enum": [ + "forward", + "reverse", + "unstranded" + ] + }, + "paired": { + "type": "boolean", + "description": "Paired-end reads or not?", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input reads for quantification.", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "index": { + "type": "string", + "format": "path", + "description": "RSEM index.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "extra_args": { + "type": "string", + "description": "Extra rsem-calculate-expression arguments in addition to the examples.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "counts_gene": { + "type": "string", + "format": "path", + "description": "Expression counts on gene level", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.counts_gene.results\"`, direction: `output`, example: `\"$id.genes.results\"`. ", + "default": "$id.$key.counts_gene.results" + }, + "counts_transcripts": { + "type": "string", + "format": "path", + "description": "Expression counts on transcript level", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.counts_transcripts.results\"`, direction: `output`, example: `\"$id.isoforms.results\"`. ", + "default": "$id.$key.counts_transcripts.results" + }, + "stat": { + "type": "string", + "format": "path", + "description": "RSEM statistics", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.stat.stat\"`, direction: `output`, example: `\"$id.stat\"`. ", + "default": "$id.$key.stat.stat" + }, + "logs": { + "type": "string", + "format": "path", + "description": "RSEM logs", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.logs.log\"`, direction: `output`, example: `\"$id.log\"`. ", + "default": "$id.$key.logs.log" + }, + "bam_star": { + "type": "string", + "format": "path", + "description": "BAM file generated by STAR (optional)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam_star.bam\"`, direction: `output`, example: `\"$id.STAR.genome.bam\"`. ", + "default": "$id.$key.bam_star.bam" + }, + "bam_genome": { + "type": "string", + "format": "path", + "description": "Genome BAM file (optional)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam_genome.bam\"`, direction: `output`, example: `\"$id.genome.bam\"`. ", + "default": "$id.$key.bam_genome.bam" + }, + "bam_transcript": { + "type": "string", + "format": "path", + "description": "Transcript BAM file (optional)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.bam_transcript.bam\"`, direction: `output`, example: `\"$id.transcript.bam\"`. ", + "default": "$id.$key.bam_transcript.bam" + }, + "sort_bam_by_read_name": { + "type": "boolean", + "description": "Sort BAM file aligned under transcript coordidate by read name", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_bam_output": { + "type": "boolean", + "description": "Do not output any BAM file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sampling_for_bam": { + "type": "boolean", + "description": "When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_genome_bam": { + "type": "boolean", + "description": "Generate a BAM file, 'sample_name.genome.bam', with alignments mapped to genomic coordinates and \nannotated with their posterior probabilities", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sort_bam_by_coordinate": { + "type": "boolean", + "description": "Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/basic options" + "basic options": { + "title": "Basic Options", + "type": "object", + "description": "No description", + "properties": { + "no_qualities": { + "type": "boolean", + "description": "Input reads do not contain quality scores.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "alignments": { + "type": "boolean", + "description": "Input file contains alignments in SAM/BAM/CRAM format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fai": { + "type": "string", + "format": "path", + "description": "If the header section of input alignment file does not contain reference sequence information, \nthis option should be turned on", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "bowtie2": { + "type": "boolean", + "description": "Use Bowtie 2 instead of Bowtie to align reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "star": { + "type": "boolean", + "description": "Use STAR to align reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hisat2_hca": { + "type": "boolean", + "description": "Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "append_names": { + "type": "boolean", + "description": "If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby '_') in files 'sample_name.isoforms.results' and 'sample_name.genes.results'.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "seed": { + "type": "integer", + "description": "Set the seed for the random number generators used in calculating posterior mean estimates and \ncredibility intervals", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "single_cell_prior": { + "type": "boolean", + "description": "By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "calc_pme": { + "type": "boolean", + "description": "Run RSEM's collapsed Gibbs sampler to calculate posterior mean estimates.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "calc_ci": { + "type": "boolean", + "description": "Calculate 95% credibility intervals and posterior mean estimates", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "quiet": { + "type": "boolean", + "description": "Suppress the output of logging information.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/aligner options" + "aligner options": { + "title": "Aligner Options", + "type": "object", + "description": "No description", + "properties": { + "seed_length": { + "type": "integer", + "description": "Seed length used by the read aligner", + "help_text": "Type: `integer`, multiple: `False`, example: `25`. " + }, + "phred64_quals": { + "type": "boolean", + "description": "Input quality scores are encoded as Phred+64 (default for GA Pipeline ver", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "solexa_quals": { + "type": "boolean", + "description": "Input quality scores are solexa encoded (from GA Pipeline ver", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bowtie_n": { + "type": "integer", + "description": "(Bowtie parameter) max # of mismatches in the seed", + "help_text": "Type: `integer`, multiple: `False`, example: `2`, choices: ``0`, `1`, `2`, `3``. ", + "enum": [ + 0, + 1, + 2, + 3 + ] + }, + "bowtie_e": { + "type": "integer", + "description": "(Bowtie parameter) max sum of mismatch quality scores across the alignment", + "help_text": "Type: `integer`, multiple: `False`, example: `99999999`. " + }, + "bowtie_m": { + "type": "integer", + "description": "(Bowtie parameter) suppress all alignments for a read if > valid alignments exist", + "help_text": "Type: `integer`, multiple: `False`, example: `200`. " + }, + "bowtie_chunkmbs": { + "type": "integer", + "description": "(Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use Bowtie's default)\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "bowtie2_mismatch_rate": { + "type": "number", + "description": "(Bowtie 2 parameter) The maximum mismatch rate allowed", + "help_text": "Type: `double`, multiple: `False`, example: `0.1`. " + }, + "bowtie2_k": { + "type": "integer", + "description": "(Bowtie 2 parameter) Find up to alignments per read", + "help_text": "Type: `integer`, multiple: `False`, example: `200`. " + }, + "bowtie2_sensitivity_level": { + "type": "string", + "description": "(Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end mode", + "help_text": "Type: `string`, multiple: `False`, example: `\"sensitive\"`, choices: ``very_fast`, `fast`, `sensitive`, `very_sensitive``. ", + "enum": [ + "very_fast", + "fast", + "sensitive", + "very_sensitive" + ] + }, + "star_gzipped_read_file": { + "type": "boolean", + "description": "Input read file(s) is compressed by gzip", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "star_bzipped_read_file": { + "type": "boolean", + "description": "Input read file(s) is compressed by bzip2", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "star_output_genome_bam": { + "type": "boolean", + "description": "Save the BAM file from STAR alignment under genomic coordinate to 'sample_name.STAR.genome.bam'", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/advanced options" + "advanced options": { + "title": "Advanced Options", + "type": "object", + "description": "No description", + "properties": { + "tag": { + "type": "string", + "description": "The name of the optional field used in the SAM input for identifying a read with too many valid \nalignments", + "help_text": "Type: `string`, multiple: `False`, example: `\"\"`. " + }, + "fragment_length_min": { + "type": "integer", + "description": "Minimum read/insert length allowed", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "fragment_length_max": { + "type": "integer", + "description": "Maximum read/insert length allowed", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "fragment_length_mean": { + "type": "integer", + "description": "(single-end data only) The mean of the fragment length distribution, which is assumed to be a \nGaussian", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "gragment_length_sd": { + "type": "number", + "description": "(single-end data only) The standard deviation of the fragment length distribution, which is \nassumed to be a Gaussian", + "help_text": "Type: `double`, multiple: `False`, example: `0.0`. " + }, + "estimate_rspd": { + "type": "boolean", + "description": "Set this option if you want to estimate the read start position distribution (RSPD) from data.\nOtherwise, RSEM will use a uniform RSPD.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_rspd_bins": { + "type": "integer", + "description": "Number of bins in the RSPD", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "gibbs_burnin": { + "type": "integer", + "description": "The number of burn-in rounds for RSEM's Gibbs sampler", + "help_text": "Type: `integer`, multiple: `False`, example: `200`. " + }, + "gibbs_number_of_samples": { + "type": "integer", + "description": "The total number of count vectors RSEM will collect from its Gibbs samplers", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "gibbs_sampling_gap": { + "type": "integer", + "description": "The number of rounds between two succinct count vectors RSEM collects", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "ci_credibility_level": { + "type": "number", + "description": "The credibility level for credibility intervals", + "help_text": "Type: `double`, multiple: `False`, example: `0.95`. " + }, + "ci_number_of_samples_per_count_vector": { + "type": "integer", + "description": "The number of read generating probability vectors sampled per sampled count vector", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + }, + "keep_intermediate_files": { + "type": "boolean", + "description": "Keep temporary files generated by RSEM", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "temporary_folder": { + "type": "string", + "description": "Set where to put the temporary files generated by RSEM", + "help_text": "Type: `string`, multiple: `False`, example: `\"sample_name.temp\"`. " + }, + "time": { + "type": "boolean", + "description": "Output time consumed by each step of RSEM to 'sample_name.time'.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/prior-enhanced rsem options" + "prior-enhanced rsem options": { + "title": "Prior-Enhanced RSEM Options", + "type": "object", + "description": "No description", + "properties": { + "run_pRSEM": { + "type": "boolean", + "description": "Running prior-enhanced RSEM (pRSEM)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "chipseq_peak_file": { + "type": "string", + "format": "path", + "description": "Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "chipseq_target_read_files": { + "type": "string", + "format": "path", + "description": "Comma-separated full path of FASTQ read file(s) for ChIP-seq target", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "chipseq_control_read_files": { + "type": "string", + "format": "path", + "description": "Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "chipseq_read_files_multi_targets": { + "type": "string", + "format": "path", + "description": "Comma-separated full path of FASTQ read files for multiple ChIP-seq targets", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "chipseq_bed_files_multi_targets": { + "type": "string", + "format": "path", + "description": "Comma-separated full path of BED files for multiple ChIP-seq targets", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "cap_stacked_chipseq_reads": { + "type": "boolean", + "description": "Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "n_max_stacked_chipseq_reads": { + "type": "integer", + "description": "The maximum number of stacked ChIP-seq reads to keep", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "partition_model": { + "type": "string", + "description": "A keyword to specify the partition model used by prior-enhanced RSEM", + "help_text": "Type: `string`, multiple: `False`, example: `\"pk\"`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/basic options" + }, + { + "$ref": "#/$defs/aligner options" + }, + { + "$ref": "#/$defs/advanced options" + }, + { + "$ref": "#/$defs/prior-enhanced rsem options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index 7f8202f6..d0475729 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -419,9 +414,9 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -446,6 +441,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index a384d9a4..94b60d3f 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -3475,9 +3467,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3493,6 +3485,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json index 1d5c516f..0ffe3a4f 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json @@ -1,321 +1,197 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rsem_prepare_reference", -"description": "RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "reference_fasta_files": { - "type": - "string", - "description": "Type: List of `file`, required, example: `read1.fasta`, multiple_sep: `\";\"`. Semi-colon separated list of Multi-FASTA formatted files OR a directory name", - "help_text": "Type: List of `file`, required, example: `read1.fasta`, multiple_sep: `\";\"`. Semi-colon separated list of Multi-FASTA formatted files OR a directory name. If a directory name is specified, RSEM will read all files with suffix \".fa\" or \".fasta\" in this directory. The files should contain either the sequences of transcripts or an entire genome, depending on whether the \u0027--gtf\u0027 option is used.\n" - - } - - - , - "reference_name": { - "type": - "string", - "description": "Type: `string`, required, example: `/ref/mm9`. The name of the reference used", - "help_text": "Type: `string`, required, example: `/ref/mm9`. The name of the reference used. RSEM will generate several reference-related files that are prefixed by this name. This name can contain path information (e.g. \u0027/ref/mm9\u0027).\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Directory containing reference files generated by RSEM." - , - "default":"$id.$key.output" - } - - -} -}, - - - "other options" : { - "title": "Other options", - "type": "object", - "description": "No description", - "properties": { - - - "gtf": { - "type": - "string", - "description": "Type: `file`, example: `annotations.gtf`. Assume that \u0027reference_fasta_files\u0027 contains the sequence of a genome, and extract transcript reference sequences using the gene annotations specified in the GTF file", - "help_text": "Type: `file`, example: `annotations.gtf`. Assume that \u0027reference_fasta_files\u0027 contains the sequence of a genome, and extract transcript reference sequences using the gene annotations specified in the GTF file. If this and \u0027--gff3\u0027 options are not provided, RSEM will assume \u0027reference_fasta_files\u0027 contains the reference transcripts. In this case, RSEM assumes that name of each sequence in the Multi-FASTA files is its transcript_id." - - } - - - , - "gff3": { - "type": - "string", - "description": "Type: `file`, example: `annotations.gff`. GFF3 annotation file", - "help_text": "Type: `file`, example: `annotations.gff`. GFF3 annotation file. Converted to GTF format with the file name \u0027reference_name.gtf\u0027. Please make sure that \u0027reference_name.gtf\u0027 does not exist." - - } - - - , - "gff3_rna_patterns": { - "type": - "string", - "description": "Type: List of `string`, example: `mRNA;rRNA`, multiple_sep: `\";\"`. List of transcript categories (separated by semi-colon)", - "help_text": "Type: List of `string`, example: `mRNA;rRNA`, multiple_sep: `\";\"`. List of transcript categories (separated by semi-colon). Only transcripts that match the string will be extracted." - - } - - - , - "gff3_genes_as_transcripts": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes", - "help_text": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes. RSEM will assume each gene as a unique transcript when it converts the GFF3 file into GTF format." - , - "default":false - } - - - , - "trusted_sources": { - "type": - "string", - "description": "Type: List of `string`, example: `ENSEMBL;HAVANA`, multiple_sep: `\";\"`. List of trusted sources (separated by semi-colon)", - "help_text": "Type: List of `string`, example: `ENSEMBL;HAVANA`, multiple_sep: `\";\"`. List of trusted sources (separated by semi-colon). Only transcripts coming from these sources will be extracted. If this option is off, all sources are accepted." - - } - - - , - "transcript_to_gene_map": { - "type": - "string", - "description": "Type: `file`, example: `isoforms.txt`. Use information from this file to map from transcript (isoform) ids to gene ids", - "help_text": "Type: `file`, example: `isoforms.txt`. Use information from this file to map from transcript (isoform) ids to gene ids. Each line of this file should be of the form: \n gene_id transcript_id\nwith the two fields separated by a tab character.\nIf you are using a GTF file for the \"UCSC Genes\" gene set from the UCSC Genome Browser, then the \"knownIsoforms.txt\" file (obtained from the \"Downloads\" section of the UCSC Genome Browser site) is of this format. \nIf this option is off, then the mapping of isoforms to genes depends on whether the \u0027--gtf\u0027 option is specified. If \u0027--gtf\u0027 is specified, then RSEM uses the \"gene_id\" and \"transcript_id\" attributes in the GTF file. Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.\n" - - } - - - , - "allele_to_gene_map": { - "type": - "string", - "description": "Type: `file`. Use information from \u003cfile\u003e to provide gene_id and transcript_id information for each allele-specific transcript", - "help_text": "Type: `file`. Use information from \u003cfile\u003e to provide gene_id and transcript_id information for each allele-specific transcript. Each line of \u003cfile\u003e should be of the form:\n gene_id transcript_id allele_id\nwith the fields separated by a tab character.\nThis option is designed for quantifying allele-specific expression. It is only valid if \u0027--gtf\u0027 option is not specified. allele_id should be the sequence names presented in the Multi-FASTA-formatted files.\n" - - } - - - , - "polyA": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms", - "help_text": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms. The length of poly(A) tail added is specified by \u0027--polyA-length\u0027 option. STAR aligner users may not want to use this option." - , - "default":false - } - - - , - "polyA_length": { - "type": - "integer", - "description": "Type: `integer`, example: `125`. The length of the poly(A) tails to be added", - "help_text": "Type: `integer`, example: `125`. The length of the poly(A) tails to be added." - - } - - - , - "no_polyA_subset": { - "type": - "string", - "description": "Type: `file`, example: `transcript_ids.txt`. Only meaningful if \u0027--polyA\u0027 is specified", - "help_text": "Type: `file`, example: `transcript_ids.txt`. Only meaningful if \u0027--polyA\u0027 is specified. Do not add poly(A) tails to those transcripts listed in this file containing a list of transcript_ids." - - } - - - , - "bowtie": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build Bowtie indices", - "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie indices." - , - "default":false - } - - - , - "bowtie2": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices", - "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices." - , - "default":false - } - - - , - "star": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build STAR indices", - "help_text": "Type: `boolean_true`, default: `false`. Build STAR indices." - , - "default":false - } - - - , - "star_sjdboverhang": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. Length of the genomic sequence around annotated junction", - "help_text": "Type: `integer`, example: `100`. Length of the genomic sequence around annotated junction. It is only used for STAR to build splice junctions database and not needed for Bowtie or Bowtie2. It will be passed as the --sjdbOverhang option to STAR. According to STAR\u0027s manual, its ideal value is max(ReadLength)-1, e.g. for 2x101 paired-end reads, the ideal value is 101-1=100. In most cases, the default value of 100 will work as well as the ideal value. (Default is 100)" - - } - - - , - "hisat2_hca": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline", - "help_text": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline." - , - "default":false - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information", - "help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information." - , - "default":false - } - - -} -}, - - - "prior-enhanced rsem options" : { - "title": "Prior-enhanced RSEM options", - "type": "object", - "description": "No description", - "properties": { - - - "prep_pRSEM": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms", - "help_text": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms. The index files will be used for aligning ChIP-seq reads in prior-enhanced RSEM and the training set isoforms will be used for learning prior. A path to Bowtie executables and a mappability file in bigWig format are required when this option is on. Currently, Bowtie2 is not supported for prior-enhanced RSEM." - , - "default":false - } - - - , - "mappability_bigwig_file": { - "type": - "string", - "description": "Type: `file`. Full path to a whole-genome mappability file in bigWig format", - "help_text": "Type: `file`. Full path to a whole-genome mappability file in bigWig format. This file is required for running prior-enhanced RSEM. It is used for selecting a training set of isoforms for prior-learning. This file can be either downloaded from UCSC Genome Browser or generated by GEM (Derrien et al., 2012, PLoS One)." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "rsem_prepare_reference", + "description": "RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "reference_fasta_files": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Semi-colon separated list of Multi-FASTA formatted files OR a directory name", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"read1.fasta\"]`. " + }, + "reference_name": { + "type": "string", + "description": "The name of the reference used", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"/ref/mm9\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Directory containing reference files generated by RSEM.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/other options" + "other options": { + "title": "Other options", + "type": "object", + "description": "No description", + "properties": { + "gtf": { + "type": "string", + "format": "path", + "description": "Assume that 'reference_fasta_files' contains the sequence of a genome, and extract transcript reference sequences using the gene annotations specified in the GTF file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"annotations.gtf\"`. " + }, + "gff3": { + "type": "string", + "format": "path", + "description": "GFF3 annotation file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"annotations.gff\"`. " + }, + "gff3_rna_patterns": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of transcript categories (separated by semi-colon)", + "help_text": "Type: `string`, multiple: `True`, example: `[\"mRNA;rRNA\"]`. " + }, + "gff3_genes_as_transcripts": { + "type": "boolean", + "description": "This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "trusted_sources": { + "type": "array", + "items": { + "type": "string" + }, + "description": "List of trusted sources (separated by semi-colon)", + "help_text": "Type: `string`, multiple: `True`, example: `[\"ENSEMBL;HAVANA\"]`. " + }, + "transcript_to_gene_map": { + "type": "string", + "format": "path", + "description": "Use information from this file to map from transcript (isoform) ids to gene ids", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"isoforms.txt\"`. " + }, + "allele_to_gene_map": { + "type": "string", + "format": "path", + "description": "Use information from to provide gene_id and transcript_id information for each allele-specific transcript", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "polyA": { + "type": "boolean", + "description": "Add poly(A) tails to the end of all reference isoforms", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "polyA_length": { + "type": "integer", + "description": "The length of the poly(A) tails to be added.", + "help_text": "Type: `integer`, multiple: `False`, example: `125`. " + }, + "no_polyA_subset": { + "type": "string", + "format": "path", + "description": "Only meaningful if '--polyA' is specified", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"transcript_ids.txt\"`. " + }, + "bowtie": { + "type": "boolean", + "description": "Build Bowtie indices.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bowtie2": { + "type": "boolean", + "description": "Build Bowtie 2 indices.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "star": { + "type": "boolean", + "description": "Build STAR indices.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "star_sjdboverhang": { + "type": "integer", + "description": "Length of the genomic sequence around annotated junction", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "hisat2_hca": { + "type": "boolean", + "description": "Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "quiet": { + "type": "boolean", + "description": "Suppress the output of logging information.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/prior-enhanced rsem options" + "prior-enhanced rsem options": { + "title": "Prior-enhanced RSEM options", + "type": "object", + "description": "No description", + "properties": { + "prep_pRSEM": { + "type": "boolean", + "description": "A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mappability_bigwig_file": { + "type": "string", + "format": "path", + "description": "Full path to a whole-genome mappability file in bigWig format", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/other options" + }, + { + "$ref": "#/$defs/prior-enhanced rsem options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index a34ee171..c822e8e5 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -178,9 +173,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -205,6 +200,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 30f2ed1b..b1aa288c 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3266,9 +3258,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3284,6 +3276,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json index 4b31a3da..1018d56d 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json @@ -1,105 +1,64 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rseqc_bamstat", -"description": "Generate statistics from a bam file.", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input_file": { - "type": - "string", - "description": "Type: `file`, required. Input alignment file in BAM or SAM format", - "help_text": "Type: `file`, required. Input alignment file in BAM or SAM format." - - } - - - , - "mapq": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads", - "help_text": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: \u002730\u0027.\n" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics", - "help_text": "Type: `file`, default: `$id.$key.output`. Output file (txt) with mapping quality statistics." - , - "default":"$id.$key.output" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "rseqc_bamstat", + "description": "Generate statistics from a bam file.", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input_file": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input alignment file in BAM or SAM format.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "mapq": { + "type": "integer", + "description": "Minimum mapping quality (phred scaled) to determine uniquely mapped reads", + "help_text": "Type: `integer`, multiple: `False`, example: `30`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file (txt) with mapping quality statistics.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index b0af3447..bef50283 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -204,9 +199,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -231,6 +226,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 2a989599..ce41b367 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3299,9 +3291,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3317,6 +3309,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json index 1ab703cb..c3bd67dc 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json @@ -1,139 +1,86 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rseqc_inferexperiment", -"description": "Infer strandedness from sequencing reads\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input_file": { - "type": - "string", - "description": "Type: `file`, required. input alignment file in BAM or SAM format", - "help_text": "Type: `file`, required. input alignment file in BAM or SAM format" - - } - - - , - "refgene": { - "type": - "string", - "description": "Type: `file`, required. Reference gene model in bed format", - "help_text": "Type: `file`, required. Reference gene model in bed format" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report", - "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report." - , - "default":"$id.$key.output.txt" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "sample_size": { - "type": - "integer", - "description": "Type: `integer`, example: `200000`. Number of reads sampled from SAM/BAM file", - "help_text": "Type: `integer`, example: `200000`. Number of reads sampled from SAM/BAM file. Default: 200000\n" - - } - - - , - "mapq": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads", - "help_text": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads. Default: 30\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "rseqc_inferexperiment", + "description": "Infer strandedness from sequencing reads\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input_file": { + "type": "string", + "format": "path", + "exists": true, + "description": "input alignment file in BAM or SAM format", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "refgene": { + "type": "string", + "format": "path", + "exists": true, + "description": "Reference gene model in bed format", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file (txt) of strandness report.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"$id.strandedness.txt\"`. ", + "default": "$id.$key.output.txt" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "sample_size": { + "type": "integer", + "description": "Number of reads sampled from SAM/BAM file", + "help_text": "Type: `integer`, multiple: `False`, example: `200000`. " + }, + "mapq": { + "type": "integer", + "description": "Minimum mapping quality (phred scaled) to determine uniquely mapped reads", + "help_text": "Type: `integer`, multiple: `False`, example: `30`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml index 74d2419c..b7454451 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Input" arguments: @@ -297,9 +292,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_inner_distance" executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -324,6 +319,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/rseqc/rseqc_inner_distance/main.nf b/target/nextflow/rseqc/rseqc_inner_distance/main.nf index 9e79f984..39b5a689 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/main.nf +++ b/target/nextflow/rseqc/rseqc_inner_distance/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3399,9 +3391,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inner_distance", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3417,6 +3409,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json index 6bcd0c8a..ddbd9763 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json @@ -1,209 +1,124 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "rseqc_inner_distance", -"description": "Calculate inner distance between read pairs.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input_file": { - "type": - "string", - "description": "Type: `file`, required. input alignment file in BAM or SAM format", - "help_text": "Type: `file`, required. input alignment file in BAM or SAM format" - - } - - - , - "refgene": { - "type": - "string", - "description": "Type: `file`, required. Reference gene model in bed format", - "help_text": "Type: `file`, required. Reference gene model in bed format" - - } - - - , - "sample_size": { - "type": - "integer", - "description": "Type: `integer`, example: `1000000`. Numer of reads sampled from SAM/BAM file, default = 1000000", - "help_text": "Type: `integer`, example: `1000000`. Numer of reads sampled from SAM/BAM file, default = 1000000." - - } - - - , - "mapq": { - "type": - "integer", - "description": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30", - "help_text": "Type: `integer`, example: `30`. Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30." - - } - - - , - "lower_bound": { - "type": - "integer", - "description": "Type: `integer`, example: `-250`. Lower bound of inner distance (bp)", - "help_text": "Type: `integer`, example: `-250`. Lower bound of inner distance (bp). This option is used for ploting histograme, default=-250." - - } - - - , - "upper_bound": { - "type": - "integer", - "description": "Type: `integer`, example: `250`. Upper bound of inner distance (bp)", - "help_text": "Type: `integer`, example: `250`. Upper bound of inner distance (bp). This option is used for ploting histograme, default=250." - - } - - - , - "step": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. Step size (bp) of histograme", - "help_text": "Type: `integer`, example: `5`. Step size (bp) of histograme. This option is used for plotting histogram, default=5." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_prefix": { - "type": - "string", - "description": "Type: `string`, required. Rrefix of output files", - "help_text": "Type: `string`, required. Rrefix of output files." - - } - - - , - "output_stats": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_stats`. output file (txt) with summary statistics of inner distances of paired reads" - , - "default":"$id.$key.output_stats" - } - - - , - "output_dist": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_dist`. output file (txt) with inner distances of all paired reads" - , - "default":"$id.$key.output_dist" - } - - - , - "output_freq": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_freq`. output file (txt) with frequencies of inner distances of all paired reads" - , - "default":"$id.$key.output_freq" - } - - - , - "output_plot": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads" - , - "default":"$id.$key.output_plot" - } - - - , - "output_plot_r": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads", - "help_text": "Type: `file`, default: `$id.$key.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads" - , - "default":"$id.$key.output_plot_r" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "rseqc_inner_distance", + "description": "Calculate inner distance between read pairs.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input_file": { + "type": "string", + "format": "path", + "exists": true, + "description": "input alignment file in BAM or SAM format", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "refgene": { + "type": "string", + "format": "path", + "exists": true, + "description": "Reference gene model in bed format", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "sample_size": { + "type": "integer", + "description": "Numer of reads sampled from SAM/BAM file, default = 1000000.", + "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. " + }, + "mapq": { + "type": "integer", + "description": "Minimum mapping quality (phred scaled) to determine uniquely mapped reads, default=30.", + "help_text": "Type: `integer`, multiple: `False`, example: `30`. " + }, + "lower_bound": { + "type": "integer", + "description": "Lower bound of inner distance (bp)", + "help_text": "Type: `integer`, multiple: `False`, example: `-250`. " + }, + "upper_bound": { + "type": "integer", + "description": "Upper bound of inner distance (bp)", + "help_text": "Type: `integer`, multiple: `False`, example: `250`. " + }, + "step": { + "type": "integer", + "description": "Step size (bp) of histograme", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output_prefix": { + "type": "string", + "description": "Rrefix of output files.", + "help_text": "Type: `string`, multiple: `False`, required. " + }, + "output_stats": { + "type": "string", + "format": "path", + "description": "output file (txt) with summary statistics of inner distances of paired reads", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_stats\"`, direction: `output`. ", + "default": "$id.$key.output_stats" + }, + "output_dist": { + "type": "string", + "format": "path", + "description": "output file (txt) with inner distances of all paired reads", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_dist\"`, direction: `output`. ", + "default": "$id.$key.output_dist" + }, + "output_freq": { + "type": "string", + "format": "path", + "description": "output file (txt) with frequencies of inner distances of all paired reads", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_freq\"`, direction: `output`. ", + "default": "$id.$key.output_freq" + }, + "output_plot": { + "type": "string", + "format": "path", + "description": "output file (pdf) with histogram plot of of inner distances of all paired reads", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_plot\"`, direction: `output`. ", + "default": "$id.$key.output_plot" + }, + "output_plot_r": { + "type": "string", + "format": "path", + "description": "output file (R) with script of histogram plot of of inner distances of all paired reads", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_plot_r\"`, direction: `output`. ", + "default": "$id.$key.output_plot_r" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index a2da7082..3411f155 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Inputs" arguments: @@ -280,9 +275,9 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -307,6 +302,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index de2d261b..03f3215b 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -3359,9 +3351,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3377,6 +3369,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/salmon/salmon_index/nextflow_schema.json b/target/nextflow/salmon/salmon_index/nextflow_schema.json index 5e67d15f..110ec0e9 100644 --- a/target/nextflow/salmon/salmon_index/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_index/nextflow_schema.json @@ -1,211 +1,122 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "salmon_index", -"description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "genome": { - "type": - "string", - "description": "Type: `file`, example: `genome.fasta`. Genome of the organism to prepare the set of decoy sequences", - "help_text": "Type: `file`, example: `genome.fasta`. Genome of the organism to prepare the set of decoy sequences. Required to build decoy-aware transcriptome.\n" - - } - - - , - "transcripts": { - "type": - "string", - "description": "Type: `file`, required, example: `transcriptome.fasta`. Transcript fasta file", - "help_text": "Type: `file`, required, example: `transcriptome.fasta`. Transcript fasta file.\n" - - } - - - , - "kmer_len": { - "type": - "integer", - "description": "Type: `integer`, example: `31`. The size of k-mers that should be used for the quasi index", - "help_text": "Type: `integer`, example: `31`. The size of k-mers that should be used for the quasi index.\n" - - } - - - , - "gencode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character", - "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n" - , - "default":false - } - - - , - "features": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character", - "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character. These reduced names will be used in the output and when looking for the sequence of the features.GTF.\n" - , - "default":false - } - - - , - "keep_duplicates": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts", - "help_text": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts. If this flag is passed, then duplicate transcripts that appear in the input will be retained and quantified separately.\n" - , - "default":false - } - - - , - "keep_fixed_fasta": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc", - "help_text": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing.\n" - , - "default":false - } - - - , - "filter_size": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. The size of the Bloom filter that will be used by TwoPaCo during indexing", - "help_text": "Type: `integer`, example: `-1`. The size of the Bloom filter that will be used by TwoPaCo during indexing. The filter will be of size 2^{filter_size}. The default value of -1 means that the filter size will be automatically set based on the number of distinct k-mers in the input, as estimated by nthll.\n" - - } - - - , - "sparse": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment", - "help_text": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment.\n" - , - "default":false - } - - - , - "decoys": { - "type": - "string", - "description": "Type: `file`, example: `decoys.txt`. Treat these sequences ids from the reference as the decoys that may have sequence homologous to some known transcript", - "help_text": "Type: `file`, example: `decoys.txt`. Treat these sequences ids from the reference as the decoys that may have sequence homologous to some known transcript. For example in case of the genome, provide a list of chromosome names (one per line).\n" - - } - - - , - "no_clip": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences.\n" - , - "default":false - } - - - , - "type": { - "type": - "string", - "description": "Type: `string`, example: `puff`. The type of index to build; the only option is \"puff\" in this version of salmon", - "help_text": "Type: `string`, example: `puff`. The type of index to build; the only option is \"puff\" in this version of salmon.\n" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n", - "help_text": "Type: `file`, required, default: `$id.$key.index`, example: `Salmon_index`. Salmon index\n" - , - "default":"$id.$key.index" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "salmon_index", + "description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "genome": { + "type": "string", + "format": "path", + "description": "Genome of the organism to prepare the set of decoy sequences", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta\"`. " + }, + "transcripts": { + "type": "string", + "format": "path", + "exists": true, + "description": "Transcript fasta file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome.fasta\"`. " + }, + "kmer_len": { + "type": "integer", + "description": "The size of k-mers that should be used for the quasi index.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `31`. " + }, + "gencode": { + "type": "boolean", + "description": "This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first '|' character", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "features": { + "type": "boolean", + "description": "This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first 'tab' character", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep_duplicates": { + "type": "boolean", + "description": "This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep_fixed_fasta": { + "type": "boolean", + "description": "Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "filter_size": { + "type": "integer", + "description": "The size of the Bloom filter that will be used by TwoPaCo during indexing", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "sparse": { + "type": "boolean", + "description": "Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "decoys": { + "type": "string", + "format": "path", + "description": "Treat these sequences ids from the reference as the decoys that may have sequence homologous to some known transcript", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"decoys.txt\"`. " + }, + "no_clip": { + "type": "boolean", + "description": "Don't clip poly-A tails from the ends of target sequences.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "type": { + "type": "string", + "description": "The type of index to build; the only option is \"puff\" in this version of salmon.\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"puff\"`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "string", + "format": "path", + "description": "Salmon index\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.index\"`, direction: `output`, example: `\"Salmon_index\"`. ", + "default": "$id.$key.index" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 4856817d..96cd0183 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Common input options" arguments: @@ -1176,9 +1171,9 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -1203,6 +1198,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 9c51d1ae..4c2acbf3 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -4194,9 +4186,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -4212,6 +4204,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/salmon/salmon_quant/nextflow_schema.json b/target/nextflow/salmon/salmon_quant/nextflow_schema.json index 2b1c3f37..7477456d 100644 --- a/target/nextflow/salmon/salmon_quant/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_quant/nextflow_schema.json @@ -1,1119 +1,656 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "salmon_quant", -"description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n", -"type": "object", -"definitions": { - - - - "common input options" : { - "title": "Common input options", - "type": "object", - "description": "No description", - "properties": { - - - "lib_type": { - "type": - "string", - "description": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library", - "help_text": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n", - "enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"] - - , - "default":"A" - } - - -} -}, - - - "mapping input options" : { - "title": "Mapping input options", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "string", - "description": "Type: `file`, example: `transcriptome_index`. Salmon index", - "help_text": "Type: `file`, example: `transcriptome_index`. Salmon index.\n" - - } - - - , - "unmated_reads": { - "type": - "string", - "description": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\";\"`. List of files containing unmated reads of (e", - "help_text": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\";\"`. List of files containing unmated reads of (e.g. single-end reads).\n" - - } - - - , - "mates1": { - "type": - "string", - "description": "Type: List of `file`, example: `sample_1.fq.gz`, multiple_sep: `\";\"`. File containing the #1 mates", - "help_text": "Type: List of `file`, example: `sample_1.fq.gz`, multiple_sep: `\";\"`. File containing the #1 mates.\n" - - } - - - , - "mates2": { - "type": - "string", - "description": "Type: List of `file`, example: `sample_2.fq.gz`, multiple_sep: `\";\"`. File containing the #2 mates", - "help_text": "Type: List of `file`, example: `sample_2.fq.gz`, multiple_sep: `\";\"`. File containing the #2 mates.\n" - - } - - -} -}, - - - "alignment input options" : { - "title": "Alignment input options", - "type": "object", - "description": "No description", - "properties": { - - - "discard_orphans": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]", - "help_text": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist.\n" - , - "default":false - } - - - , - "alignments": { - "type": - "string", - "description": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\";\"`. Input alignment (BAM) file(s)", - "help_text": "Type: List of `file`, example: `sample.fq.gz`, multiple_sep: `\";\"`. Input alignment (BAM) file(s).\n" - - } - - - , - "eqclasses": { - "type": - "string", - "description": "Type: `file`. input salmon weighted equivalence class file", - "help_text": "Type: `file`. input salmon weighted equivalence class file.\n" - - } - - - , - "targets": { - "type": - "string", - "description": "Type: `file`, example: `transcripts.fasta`. FASTA format file containing target transcripts", - "help_text": "Type: `file`, example: `transcripts.fasta`. FASTA format file containing target transcripts.\n" - - } - - - , - "ont": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n", - "help_text": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n" - , - "default":false - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory", - "help_text": "Type: `file`, required, default: `$id.$key.output`, example: `quant_output`. Output quantification directory.\n" - , - "default":"$id.$key.output" - } - - - , - "quant_results": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file", - "help_text": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n" - , - "default":"$id.$key.quant_results.sf" - } - - -} -}, - - - "basic options" : { - "title": "Basic options", - "type": "object", - "description": "No description", - "properties": { - - - "seq_bias": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction", - "help_text": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction.\n" - , - "default":false - } - - - , - "gc_bias": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads]", - "help_text": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads].\n" - , - "default":false - } - - - , - "pos_bias": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform positional bias correction", - "help_text": "Type: `boolean_true`, default: `false`. Perform positional bias correction.\n" - , - "default":false - } - - - , - "incompat_prior": { - "type": - "number", - "description": "Type: `double`, example: `0.0`. Set the prior probability that an alignment that disagrees with the specified library type (--lib_type) results from the true fragment origin", - "help_text": "Type: `double`, example: `0.0`. Set the prior probability that an alignment that disagrees with the specified library type (--lib_type) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be \"impossible\", while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do.\n" - - } - - - , - "gene_map": { - "type": - "string", - "description": "Type: `file`, example: `gene_map.gtf`. File containing a mapping of transcripts to genes", - "help_text": "Type: `file`, example: `gene_map.gtf`. File containing a mapping of transcripts to genes. If this file is provided salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab. The extension of the file is used to determine how the file should be parsed. Files ending in \u0027.gtf\u0027, \u0027.gff\u0027 or \u0027.gff3\u0027 are assumed to be in GTF format; files with any other extension are assumed to be in the simple format. In GTF / GFF format, the \"transcript_id\" is assumed to contain the transcript identifier and the \"gene_id\" is assumed to contain the corresponding gene identifier.\n" - - } - - - , - "aux_target_file": { - "type": - "string", - "description": "Type: `file`, example: `auxilary_targets.txt`. A file containing a list of \"auxiliary\" targets", - "help_text": "Type: `file`, example: `auxilary_targets.txt`. A file containing a list of \"auxiliary\" targets. These are valid targets (i.e., not decoys) to which fragments are allowed to map and be assigned, and which will be quantified, but for which auxiliary models like sequence-specific and fragment-GC bias correction should not be applied.\n" - - } - - - , - "meta": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data", - "help_text": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.\n" - , - "default":false - } - - - , - "score_exp": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. The factor by which sub-optimal alignment scores are downweighted to produce a probability", - "help_text": "Type: `double`, example: `1.0`. The factor by which sub-optimal alignment scores are downweighted to produce a probability. If the best alignment score for the current read is S, and the score for a particular alignment is w, then the probability will be computed porportional to exp( - scoreExp * (S-w) ).\n" - - } - - -} -}, - - - "options specific to mapping mode" : { - "title": "Options specific to mapping mode", - "type": "object", - "description": "No description", - "properties": { - - - "discard_orphans_quasi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist. This flag is independent of the option to write the orphaned mappings to file (--writeOrphanLinks).\n" - , - "default":false - } - - - , - "consensus_slack": { - "type": - "number", - "description": "Type: `double`, example: `0.35`. [selective-alignment mode only] \nThe amount of slack allowed in the selective-alignment filtering mechanism", - "help_text": "Type: `double`, example: `0.35`. [selective-alignment mode only] \nThe amount of slack allowed in the selective-alignment filtering mechanism. If this is set to a fraction, X, greater than 0 (and in [0,1)), then uniMEM chains with scores below (100 * X)% of the best chain score for a read, and read pairs with a sum of chain scores below (100 * X)% of the best chain score for a read pair will be discounted as a mapping candidates. The default value of this option is 0.35.\n" - - } - - - , - "pre_merge_chain_sub_thresh": { - "type": - "number", - "description": "Type: `double`, example: `0.75`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", - "help_text": "Type: `double`, example: `0.75`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping. Specifically, if the best chain for a read (or read-end in paired-end mode) to target t has score X_t, then all chains for this read with score \u003e= X_t * preMergeChainSubThresh will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1].\n" - - } - - - , - "post_merge_chain_sub_thresh": { - "type": - "number", - "description": "Type: `double`, example: `0.9`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", - "help_text": "Type: `double`, example: `0.9`. [selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping. This is different than post_merge_chain_sub_thresh, because this is applied to pairs of chains (from the ends of paired-end reads) after merging (i.e. after checking concordancy constraints etc.). Specifically, if the best chain pair to target t has score X_t, then all chain pairs for this read pair with score \u003e= X_t * post_merge_chain_sub_thresh will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1]. Note: This option is only meaningful for paired-end libraries, and is ignored for single-end libraries.\n" - - } - - - , - "orphan_chain_sub_thresh": { - "type": - "number", - "description": "Type: `double`, example: `0.95`. [selective-alignment mode only]\nThis threshold sets a global sub-optimality threshold for chains corresponding to orphan mappings", - "help_text": "Type: `double`, example: `0.95`. [selective-alignment mode only]\nThis threshold sets a global sub-optimality threshold for chains corresponding to orphan mappings. That is, if the merging procedure results in no concordant mappings then only orphan mappings with a chain score \u003e= orphan_chain_sub_thresh * bestChainScore will be retained and passed to subsequent mapping phases. This value must be in the range [0, 1]. Note: This option is only meaningful for paired-end libraries, and is ignored for single-end libraries.\n" - - } - - - , - "min_score_fraction": { - "type": - "number", - "description": "Type: `double`, example: `0.65`. [selective-alignment mode only]\nThe fraction of the optimal possible alignment score that a mapping must achieve in order to be considered \"valid\" --- should be in (0,1]", - "help_text": "Type: `double`, example: `0.65`. [selective-alignment mode only]\nThe fraction of the optimal possible alignment score that a mapping must achieve in order to be considered \"valid\" --- should be in (0,1]. Default 0.65\n" - - } - - - , - "mismatch_seed_skip": { - "type": - "integer", - "description": "Type: `integer`, example: `3`. [selective-alignment mode only]\nAfter a k-mer hit is extended to a uni-MEM, the uni-MEM extension can terminate for one of 3 reasons; the end of the read, the end of the unitig, or a mismatch", - "help_text": "Type: `integer`, example: `3`. [selective-alignment mode only]\nAfter a k-mer hit is extended to a uni-MEM, the uni-MEM extension can terminate for one of 3 reasons; the end of the read, the end of the unitig, or a mismatch. If the extension ends because of a mismatch, this is likely the result of a sequencing error. To avoid looking up many k-mers that will likely fail to be located in the index, the search procedure skips by a factor of mismatch_seed_skip until it either (1) finds another match or (2) is k-bases past the mismatch position. This value controls that skip length. A smaller value can increase sensitivity, while a larger value can speed up seeding.\n" - - } - - - , - "disable_chaining_heuristic": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found. This speeds up the seed (MEM) chaining step, but may result in sub-optimal chains in complex situations (e.g. sequences with many repeats and overlapping repeats). Passing this flag will disable the chaining heuristic, and perform the full chaining dynamic program, guaranteeing the optimal chain is found in this step.\n" - , - "default":false - } - - - , - "decoy_threshold": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. [selective-alignment mode only]\nFor an alignemnt to an annotated transcript to be considered invalid, it must have an alignment score \u003c (decoy_threshold * bestDecoyScore)", - "help_text": "Type: `double`, example: `1.0`. [selective-alignment mode only]\nFor an alignemnt to an annotated transcript to be considered invalid, it must have an alignment score \u003c (decoy_threshold * bestDecoyScore). A value of 1.0 means that any alignment strictly worse than the best decoy alignment will be discarded. A smaller value will allow reads to be allocated to transcripts even if they strictly align better to the decoy sequence.\n" - - } - - - , - "ma": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a match between read and reference nucleotides in an alignment", - "help_text": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a match between read and reference nucleotides in an alignment.\n" - - } - - - , - "mp": { - "type": - "integer", - "description": "Type: `integer`, example: `-4`. [selective-alignment mode only]\nThe value given to a mis-match between read and reference nucleotides in an alignment", - "help_text": "Type: `integer`, example: `-4`. [selective-alignment mode only]\nThe value given to a mis-match between read and reference nucleotides in an alignment.\n" - - } - - - , - "go": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. [selective-alignment mode only]\nThe value given to a gap opening in an alignment", - "help_text": "Type: `integer`, example: `6`. [selective-alignment mode only]\nThe value given to a gap opening in an alignment.\n" - - } - - - , - "ge": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a gap extension in an alignment", - "help_text": "Type: `integer`, example: `2`. [selective-alignment mode only]\nThe value given to a gap extension in an alignment.\n" - - } - - - , - "bandwidth": { - "type": - "integer", - "description": "Type: `integer`, example: `15`. [selective-alignment mode only]\nThe value used for the bandwidth passed to ksw2", - "help_text": "Type: `integer`, example: `15`. [selective-alignment mode only]\nThe value used for the bandwidth passed to ksw2. A smaller bandwidth can make the alignment verification run more quickly, but could possibly miss valid alignments.\n" - - } - - - , - "allow_dovetail": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings.\n" - , - "default":false - } - - - , - "recover_orphans": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity.\n" - , - "default":false - } - - - , - "mimicBT2": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimic_strictBT2 flag below.\n" - , - "default":false - } - - - , - "mimic_strictBT2": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --min_score_fraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments.\n" - , - "default":false - } - - - , - "softclip": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment. If this option is provided, then regions at the beginning or end of the read can be withheld from alignment without any effect on the resulting score (i.e. neither adding nor removing from the score). This will drastically reduce the penalty if there are mismatches at the beginning or end of the read due to e.g. low-quality bases or adapters. NOTE: Even with soft-clipping enabled, the read must still achieve a score of at least min_score_fraction * maximum achievable score, where the maximum achievable score is computed based on the full (un-clipped) read length.\n" - , - "default":false - } - - - , - "softclip_overhangs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript. In this case, the overhaning section of the read will simply be unaligned, and will not contribute or detract from the alignment score. The default policy is to force an end-to-end alignment of the entire read, so that overhanings will result in some deletion of nucleotides from the read.\n" - , - "default":false - } - - - , - "full_length_alignment": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment. This is in contrast with the default behavior which is to only perform alignment between the MEMs in the optimal chain (and before the first and after the last MEM if applicable). The default strategy forces the MEMs to belong to the alignment, but has the benefit that it can discover indels prior to the first hit shared between the read and reference. Except in very rare circumstances, the default mode should be more accurate.\n" - , - "default":false - } - - - , - "hard_filter": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score", - "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate \u0027naive\u0027 equivalence classes, rather than range factorized equivalence classes.\n" - , - "default":false - } - - - , - "min_aln_prob": { - "type": - "number", - "description": "Type: `double`, example: `1.0E-5`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed", - "help_text": "Type: `double`, example: `1.0E-5`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n" - - } - - - , - "write_mappings": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format", - "help_text": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.\n" - , - "default":false - } - - - , - "mapping_sam": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format", - "help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings" - , - "default":"$id.$key.mapping_sam.sam" - } - - - , - "write_qualities": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z)", - "help_text": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z). If this flag is provided, then the output SAM file will contain quality strings as well as read sequences. Note that this can greatly increase the size of the output file.\n" - , - "default":false - } - - - , - "hit_filter_policy": { - "type": - "string", - "description": "Type: `string`, example: `AFTER`, choices: ``BEFORE`, `AFTER`, `BOTH`, `NONE``. [selective-alignment mode only]\nDetermines the policy by which hits are filtered in selective alignment", - "help_text": "Type: `string`, example: `AFTER`, choices: ``BEFORE`, `AFTER`, `BOTH`, `NONE``. [selective-alignment mode only]\nDetermines the policy by which hits are filtered in selective alignment. Filtering hits after chaining (the default) is more sensitive, but more computationally intensive, because it performs the chaining dynamic program for all hits. Filtering before chaining is faster, but some true hits may be missed. The options are BEFORE, AFTER, BOTH and NONE.\n", - "enum": ["BEFORE", "AFTER", "BOTH", "NONE"] - - - } - - -} -}, - - - "advance options" : { - "title": "Advance options", - "type": "object", - "description": "No description", - "properties": { - - - "alternative_init_mode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm", - "help_text": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm.\n" - , - "default":false - } - - - , - "aux_dir": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e", - "help_text": "Type: `file`, default: `$id.$key.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n" - , - "default":"$id.$key.aux_dir" - } - - - , - "skip_quant": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)", - "help_text": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping).\n" - , - "default":false - } - - - , - "dump_eq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment", - "help_text": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment.\n" - , - "default":false - } - - - , - "dump_eq_weights": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file", - "help_text": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file. Note, this will dump the factorization that is actually used by salmon\u0027s offline phase for inference. If you are using range-factorized equivalence classes (the default) then the same transcript set may appear multiple times with different associated conditional probabilities.\n" - , - "default":false - } - - - , - "min_assigned_frags": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed", - "help_text": "Type: `integer`, example: `10`. The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n" - - } - - - , - "reduce_GC_memory": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content", - "help_text": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content. Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same.\n" - , - "default":false - } - - - , - "bias_speed_samp": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. The value at which the fragment length PMF is down-sampled when evaluating sequence-specific \u0026 GC fragment bias", - "help_text": "Type: `integer`, example: `5`. The value at which the fragment length PMF is down-sampled when evaluating sequence-specific \u0026 GC fragment bias. Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results.\n" - - } - - - , - "fld_max": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. The maximum fragment length to consider when building the empirical distribution\n", - "help_text": "Type: `integer`, example: `1000`. The maximum fragment length to consider when building the empirical distribution\n" - - } - - - , - "fld_mean": { - "type": - "integer", - "description": "Type: `integer`, example: `250`. The mean used in the fragment length distribution prior\n", - "help_text": "Type: `integer`, example: `250`. The mean used in the fragment length distribution prior\n" - - } - - - , - "fld_SD": { - "type": - "integer", - "description": "Type: `integer`, example: `25`. The standard deviation used in the fragment length distribution prior\n", - "help_text": "Type: `integer`, example: `25`. The standard deviation used in the fragment length distribution prior\n" - - } - - - , - "forgetting_factor": { - "type": - "number", - "description": "Type: `double`, example: `0.65`. The forgetting factor used in the online learning schedule", - "help_text": "Type: `double`, example: `0.65`. The forgetting factor used in the online learning schedule. A smallervalue results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0].\n" - - } - - - , - "init_uniform": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters", - "help_text": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters.\n" - , - "default":false - } - - - , - "max_occs_per_hit": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit occurrences won\u0027t be considered", - "help_text": "Type: `integer`, example: `1000`. When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit occurrences won\u0027t be considered.\n" - - } - - - , - "max_read_occ": { - "type": - "integer", - "description": "Type: `integer`, example: `200`. Reads \"mapping\" to more than this many places won\u0027t be considered", - "help_text": "Type: `integer`, example: `200`. Reads \"mapping\" to more than this many places won\u0027t be considered.\n" - - } - - - , - "no_length_correction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts", - "help_text": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target\u0027s length (e.g. QuantSeq)\n" - , - "default":false - } - - - , - "no_effective_length_correction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript", - "help_text": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in,the fragment length distribution is not taken into account when computing this probability.\n" - , - "default":false - } - - - , - "no_single_frag_prob": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries", - "help_text": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries. The default behavior is to consider the probability of all possible fragment lengths associated with the retained mapping. Enabling this flag (i.e. turning this default behavior off) will simply not attempt to estimate a fragment length probability in such cases.\n" - , - "default":false - } - - - , - "no_frag_length_dist": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location", - "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment\u0027s a priori probability.\n" - , - "default":false - } - - - , - "no_bias_length_threshold": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths", - "help_text": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths. This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold.\n" - , - "default":false - } - - - , - "num_bias_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `2000000`. Number of fragment mappings to use when learning the sequence-specific bias model", - "help_text": "Type: `integer`, example: `2000000`. Number of fragment mappings to use when learning the sequence-specific bias model.\n" - - } - - - , - "num_aux_model_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `5000000`. The first \u003cnum_aux_model_samples\u003e are used to train the auxiliary model parameters (e", - "help_text": "Type: `integer`, example: `5000000`. The first \u003cnum_aux_model_samples\u003e are used to train the auxiliary model parameters (e.g. fragment length distribution, bias, etc.). After ther first \u003cnum_aux_model_samples\u003e observations the auxiliary model parameters will be assumed to have converged and will be fixed.\n" - - } - - - , - "num_pre_aux_model_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `5000`. The first \u003cnumPreAuxModelSamples\u003e will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models", - "help_text": "Type: `integer`, example: `5000`. The first \u003cnumPreAuxModelSamples\u003e will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models. The purpose of ignoring the auxiliary models for the first \u003cnum_pre_aux_model_samples\u003e observations is to avoid applying these models before their parameters have been learned sufficiently well.\n" - - } - - - , - "useEM": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes", - "help_text": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes.\n" - , - "default":false - } - - - , - "useVBOpt": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n", - "help_text": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n" - , - "default":false - } - - - , - "range_factorization_bins": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts", - "help_text": "Type: `integer`, example: `4`. Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (4) corresponds to the default used in Zakeri et al. 2017 (doi: 10.1093/bioinformatics/btx262), and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4. A value of 0 signifies the use of basic rich equivalence classes.\n" - - } - - - , - "num_Gibbs_samples": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Number of Gibbs sampling rounds to perform", - "help_text": "Type: `integer`, example: `0`. Number of Gibbs sampling rounds to perform.\n" - - } - - - , - "no_Gamma_draw": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling", - "help_text": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity\n" - , - "default":false - } - - - , - "num_bootstraps": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Number of bootstrap samples to generate", - "help_text": "Type: `integer`, example: `0`. Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling.\n" - - } - - - , - "bootstrap_reproject": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts", - "help_text": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts.\n" - , - "default":false - } - - - , - "thinning_factor": { - "type": - "integer", - "description": "Type: `integer`, example: `16`. Number of steps to discard for every sample kept from the Gibbs chain", - "help_text": "Type: `integer`, example: `16`. Number of steps to discard for every sample kept from the Gibbs chain. The larger this number, the less chance that subsequent samples are auto-correlated, but the slower sampling becomes.\n" - - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong)", - "help_text": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong).\n" - , - "default":false - } - - - , - "per_transcript_prior": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i", - "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i.e. each transcript will be given a prior read count of this value)\n" - , - "default":false - } - - - , - "per_nucleotide_prior": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i", - "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i.e. each nucleotide will be given a prior read count of this value)\n" - , - "default":false - } - - - , - "sig_digits": { - "type": - "integer", - "description": "Type: `integer`, example: `3`. The number of significant digits to write when outputting the EffectiveLength and NumReads columns\n", - "help_text": "Type: `integer`, example: `3`. The number of significant digits to write when outputting the EffectiveLength and NumReads columns\n" - - } - - - , - "vb_prior": { - "type": - "number", - "description": "Type: `double`, example: `0.01`. The prior that will be used in the VBEM algorithm", - "help_text": "Type: `double`, example: `0.01`. The prior that will be used in the VBEM algorithm. This is interpreted as a per-transcript prior, unless the --per_nucleotide_prior flag is also given. If the --per_nucleotide_prior flag is given, this is used as a nucleotide-level prior. If the default is used, it will be divided by 1000 before being used as a nucleotide-level prior, i.e. the default per-nucleotide prior will be 1e-5.\n" - - } - - - , - "write_orphan_links": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads", - "help_text": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads.\n" - , - "default":false - } - - - , - "write_unmapped_names": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names", - "help_text": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names.txt in the auxiliary directory.\n" - , - "default":false - } - - -} -}, - - - "alignment-specific options" : { - "title": "Alignment-specific options", - "type": "object", - "description": "No description", - "properties": { - - - "no_error_model": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment", - "help_text": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy.\n" - , - "default":false - } - - - , - "num_error_bins": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. The number of bins into which to divide each read when learning and applying the error model", - "help_text": "Type: `integer`, example: `6`. The number of bins into which to divide each read when learning and applying the error model. For example, a value of 10 would mean that effectively, a separate error model is leared and applied to each 10th of the read, while a value of 3 would mean that a separate error model is applied to the read beginning (first third), middle (second third) and end (final third).\n" - - } - - - , - "sample_out": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Write a \"postSample", - "help_text": "Type: `boolean_true`, default: `false`. Write a \"postSample.bam\" file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you\u0027re going to perform downstream analysis of the alignments with tools which don\u0027t, themselves, take fragment assignment ambiguity into account, you should use this output.\n" - , - "default":false - } - - - , - "sample_unaligned": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample", - "help_text": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample.bam\".\n" - , - "default":false - } - - - , - "gencode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character", - "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n" - , - "default":false - } - - - , - "mapping_cache_memory_limit": { - "type": - "integer", - "description": "Type: `integer`, example: `2000000`. If the file contained fewer than this many mapped reads, then just keep the data in memory for subsequent rounds of inference", - "help_text": "Type: `integer`, example: `2000000`. If the file contained fewer than this many mapped reads, then just keep the data in memory for subsequent rounds of inference. Obviously, this value should not be too large if you wish to keep a low memory usage, but setting it large enough to accommodate all of the mapped read can substantially speed up inference on \"small\" files that contain only a few million reads.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/common input options" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "salmon_quant", + "description": "Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n", + "type": "object", + "$defs": { + "common input options": { + "title": "Common input options", + "type": "object", + "description": "No description", + "properties": { + "lib_type": { + "type": "string", + "description": "Format string describing the library.\nThe library type string consists of three parts: \n1", + "help_text": "Type: `string`, multiple: `False`, default: `\"A\"`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. ", + "enum": [ + "A", + "U", + "SF", + "SR", + "IU", + "IS", + "ISF", + "ISR", + "OU", + "OS", + "OSF", + "OSR", + "MU", + "MS", + "MSF", + "MSR" + ], + "default": "A" + } + } }, - - { - "$ref": "#/definitions/mapping input options" + "mapping input options": { + "title": "Mapping input options", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "string", + "format": "path", + "description": "Salmon index.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"transcriptome_index\"`. " + }, + "unmated_reads": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "List of files containing unmated reads of (e.g", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"sample.fq.gz\"]`. " + }, + "mates1": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "File containing the #1 mates.\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"sample_1.fq.gz\"]`. " + }, + "mates2": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "File containing the #2 mates.\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"sample_2.fq.gz\"]`. " + } + } }, - - { - "$ref": "#/definitions/alignment input options" + "alignment input options": { + "title": "Alignment input options", + "type": "object", + "description": "No description", + "properties": { + "discard_orphans": { + "type": "boolean", + "description": "Discard orphan alignments in the input [for alignment-based mode only]", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "alignments": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input alignment (BAM) file(s).\n", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"sample.fq.gz\"]`. " + }, + "eqclasses": { + "type": "string", + "format": "path", + "description": "input salmon weighted equivalence class file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "targets": { + "type": "string", + "format": "path", + "description": "FASTA format file containing target transcripts.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"transcripts.fasta\"`. " + }, + "ont": { + "type": "boolean", + "description": "Use alignment model for Oxford Nanopore long reads\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output quantification directory.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"quant_output\"`. ", + "default": "$id.$key.output" + }, + "quant_results": { + "type": "string", + "format": "path", + "description": "Salmon quantification file.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.quant_results.sf\"`, direction: `output`, example: `\"quant.sf\"`. ", + "default": "$id.$key.quant_results.sf" + } + } }, - - { - "$ref": "#/definitions/basic options" + "basic options": { + "title": "Basic options", + "type": "object", + "description": "No description", + "properties": { + "seq_bias": { + "type": "boolean", + "description": "Perform sequence-specific bias correction.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gc_bias": { + "type": "boolean", + "description": "Perform fragment GC bias correction [beta for single-end reads].\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "pos_bias": { + "type": "boolean", + "description": "Perform positional bias correction.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "incompat_prior": { + "type": "number", + "description": "Set the prior probability that an alignment that disagrees with the specified library type (--lib_type) results from the true fragment origin", + "help_text": "Type: `double`, multiple: `False`, example: `0.0`. " + }, + "gene_map": { + "type": "string", + "format": "path", + "description": "File containing a mapping of transcripts to genes", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"gene_map.gtf\"`. " + }, + "aux_target_file": { + "type": "string", + "format": "path", + "description": "A file containing a list of \"auxiliary\" targets", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"auxilary_targets.txt\"`. " + }, + "meta": { + "type": "boolean", + "description": "If you're using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "score_exp": { + "type": "number", + "description": "The factor by which sub-optimal alignment scores are downweighted to produce a probability", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + } + } }, - - { - "$ref": "#/definitions/options specific to mapping mode" + "options specific to mapping mode": { + "title": "Options specific to mapping mode", + "type": "object", + "description": "No description", + "properties": { + "discard_orphans_quasi": { + "type": "boolean", + "description": "[selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "consensus_slack": { + "type": "number", + "description": "[selective-alignment mode only] \nThe amount of slack allowed in the selective-alignment filtering mechanism", + "help_text": "Type: `double`, multiple: `False`, example: `0.35`. " + }, + "pre_merge_chain_sub_thresh": { + "type": "number", + "description": "[selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", + "help_text": "Type: `double`, multiple: `False`, example: `0.75`. " + }, + "post_merge_chain_sub_thresh": { + "type": "number", + "description": "[selective-alignment mode only] \nThe threshold of sub-optimal chains, compared to the best chain on a given target, that will be retained and passed to the next phase of mapping", + "help_text": "Type: `double`, multiple: `False`, example: `0.9`. " + }, + "orphan_chain_sub_thresh": { + "type": "number", + "description": "[selective-alignment mode only]\nThis threshold sets a global sub-optimality threshold for chains corresponding to orphan mappings", + "help_text": "Type: `double`, multiple: `False`, example: `0.95`. " + }, + "min_score_fraction": { + "type": "number", + "description": "[selective-alignment mode only]\nThe fraction of the optimal possible alignment score that a mapping must achieve in order to be considered \"valid\" --- should be in (0,1]", + "help_text": "Type: `double`, multiple: `False`, example: `0.65`. " + }, + "mismatch_seed_skip": { + "type": "integer", + "description": "[selective-alignment mode only]\nAfter a k-mer hit is extended to a uni-MEM, the uni-MEM extension can terminate for one of 3 reasons; the end of the read, the end of the unitig, or a mismatch", + "help_text": "Type: `integer`, multiple: `False`, example: `3`. " + }, + "disable_chaining_heuristic": { + "type": "boolean", + "description": "[selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "decoy_threshold": { + "type": "number", + "description": "[selective-alignment mode only]\nFor an alignemnt to an annotated transcript to be considered invalid, it must have an alignment score < (decoy_threshold * bestDecoyScore)", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + }, + "ma": { + "type": "integer", + "description": "[selective-alignment mode only]\nThe value given to a match between read and reference nucleotides in an alignment.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "mp": { + "type": "integer", + "description": "[selective-alignment mode only]\nThe value given to a mis-match between read and reference nucleotides in an alignment.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `-4`. " + }, + "go": { + "type": "integer", + "description": "[selective-alignment mode only]\nThe value given to a gap opening in an alignment.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "ge": { + "type": "integer", + "description": "[selective-alignment mode only]\nThe value given to a gap extension in an alignment.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "bandwidth": { + "type": "integer", + "description": "[selective-alignment mode only]\nThe value used for the bandwidth passed to ksw2", + "help_text": "Type: `integer`, multiple: `False`, example: `15`. " + }, + "allow_dovetail": { + "type": "boolean", + "description": "[selective-alignment mode only] \nAllow dovetailing mappings.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "recover_orphans": { + "type": "boolean", + "description": "[selective-alignment mode only] \nAttempt to recover the mates of orphaned reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mimicBT2": { + "type": "boolean", + "description": "[selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mimic_strictBT2": { + "type": "boolean", + "description": "[selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "softclip": { + "type": "boolean", + "description": "[selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "softclip_overhangs": { + "type": "boolean", + "description": "[selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "full_length_alignment": { + "type": "boolean", + "description": "[selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hard_filter": { + "type": "boolean", + "description": "[selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_aln_prob": { + "type": "number", + "description": "The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n", + "help_text": "Type: `double`, multiple: `False`, example: `1.0E-5`. " + }, + "write_mappings": { + "type": "boolean", + "description": "If this option is provided, then the selective-alignment results will be written out in SAM-compatible format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mapping_sam": { + "type": "string", + "format": "path", + "description": "Path to file that should output the selective-alignment results in SAM-compatible format", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.mapping_sam.sam\"`, direction: `output`, example: `\"mappings.sam\"`. ", + "default": "$id.$key.mapping_sam.sam" + }, + "write_qualities": { + "type": "boolean", + "description": "This flag only has meaning if mappings are being written (with --write_mappings/-z)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hit_filter_policy": { + "type": "string", + "description": "[selective-alignment mode only]\nDetermines the policy by which hits are filtered in selective alignment", + "help_text": "Type: `string`, multiple: `False`, example: `\"AFTER\"`, choices: ``BEFORE`, `AFTER`, `BOTH`, `NONE``. ", + "enum": [ + "BEFORE", + "AFTER", + "BOTH", + "NONE" + ] + } + } }, - - { - "$ref": "#/definitions/advance options" + "advance options": { + "title": "Advance options", + "type": "object", + "description": "No description", + "properties": { + "alternative_init_mode": { + "type": "boolean", + "description": "Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "aux_dir": { + "type": "string", + "format": "path", + "description": "The sub-directory of the quantification directory where auxiliary information e.g", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.aux_dir\"`, direction: `output`, example: `\"aux_info\"`. ", + "default": "$id.$key.aux_dir" + }, + "skip_quant": { + "type": "boolean", + "description": "Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dump_eq": { + "type": "boolean", + "description": "Dump the simple equivalence class counts that were computed during mapping or alignment.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dump_eq_weights": { + "type": "boolean", + "description": "Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_assigned_frags": { + "type": "integer", + "description": "The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "reduce_GC_memory": { + "type": "boolean", + "description": "If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bias_speed_samp": { + "type": "integer", + "description": "The value at which the fragment length PMF is down-sampled when evaluating sequence-specific & GC fragment bias", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "fld_max": { + "type": "integer", + "description": "The maximum fragment length to consider when building the empirical distribution\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "fld_mean": { + "type": "integer", + "description": "The mean used in the fragment length distribution prior\n", + "help_text": "Type: `integer`, multiple: `False`, example: `250`. " + }, + "fld_SD": { + "type": "integer", + "description": "The standard deviation used in the fragment length distribution prior\n", + "help_text": "Type: `integer`, multiple: `False`, example: `25`. " + }, + "forgetting_factor": { + "type": "number", + "description": "The forgetting factor used in the online learning schedule", + "help_text": "Type: `double`, multiple: `False`, example: `0.65`. " + }, + "init_uniform": { + "type": "boolean", + "description": "Initialize the offline inference with uniform parameters, rather than seeding with online parameters.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "max_occs_per_hit": { + "type": "integer", + "description": "When collecting \"hits\" (MEMs), hits having more than max_occs_per_hit occurrences won't be considered.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "max_read_occ": { + "type": "integer", + "description": "Reads \"mapping\" to more than this many places won't be considered.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `200`. " + }, + "no_length_correction": { + "type": "boolean", + "description": "Entirely disables length correction when estimating the abundance of transcripts", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_effective_length_correction": { + "type": "boolean", + "description": "Disables effective length correction when computing the probability that a fragment was generated from a transcript", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_single_frag_prob": { + "type": "boolean", + "description": "Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_frag_length_dist": { + "type": "boolean", + "description": "Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_bias_length_threshold": { + "type": "boolean", + "description": "If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_bias_samples": { + "type": "integer", + "description": "Number of fragment mappings to use when learning the sequence-specific bias model.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `2000000`. " + }, + "num_aux_model_samples": { + "type": "integer", + "description": "The first are used to train the auxiliary model parameters (e.g", + "help_text": "Type: `integer`, multiple: `False`, example: `5000000`. " + }, + "num_pre_aux_model_samples": { + "type": "integer", + "description": "The first will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models", + "help_text": "Type: `integer`, multiple: `False`, example: `5000`. " + }, + "useEM": { + "type": "boolean", + "description": "Use the traditional EM algorithm for optimization in the batch passes.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "useVBOpt": { + "type": "boolean", + "description": "Use the Variational Bayesian EM [default]\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "range_factorization_bins": { + "type": "integer", + "description": "Factorizes the likelihood used in quantification by adopting a new notion of equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "num_Gibbs_samples": { + "type": "integer", + "description": "Number of Gibbs sampling rounds to perform.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "no_Gamma_draw": { + "type": "boolean", + "description": "This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_bootstraps": { + "type": "integer", + "description": "Number of bootstrap samples to generate", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "bootstrap_reproject": { + "type": "boolean", + "description": "This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "thinning_factor": { + "type": "integer", + "description": "Number of steps to discard for every sample kept from the Gibbs chain", + "help_text": "Type: `integer`, multiple: `False`, example: `16`. " + }, + "quiet": { + "type": "boolean", + "description": "Be quiet while doing quantification (don't write informative output to the console unless something goes wrong).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "per_transcript_prior": { + "type": "boolean", + "description": "The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "per_nucleotide_prior": { + "type": "boolean", + "description": "The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sig_digits": { + "type": "integer", + "description": "The number of significant digits to write when outputting the EffectiveLength and NumReads columns\n", + "help_text": "Type: `integer`, multiple: `False`, example: `3`. " + }, + "vb_prior": { + "type": "number", + "description": "The prior that will be used in the VBEM algorithm", + "help_text": "Type: `double`, multiple: `False`, example: `0.01`. " + }, + "write_orphan_links": { + "type": "boolean", + "description": "Write the transcripts that are linked by orphaned reads.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "write_unmapped_names": { + "type": "boolean", + "description": "Write the names of un-mapped reads to the file unmapped_names.txt in the auxiliary directory.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/alignment-specific options" + "alignment-specific options": { + "title": "Alignment-specific options", + "type": "object", + "description": "No description", + "properties": { + "no_error_model": { + "type": "boolean", + "description": "Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_error_bins": { + "type": "integer", + "description": "The number of bins into which to divide each read when learning and applying the error model", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "sample_out": { + "type": "boolean", + "description": "Write a \"postSample.bam\" file in the output directory that will sample the input alignments according to the estimated transcript abundances", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sample_unaligned": { + "type": "boolean", + "description": "In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample.bam\".\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gencode": { + "type": "boolean", + "description": "This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first '|' character", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "mapping_cache_memory_limit": { + "type": "integer", + "description": "If the file contained fewer than this many mapped reads, then just keep the data in memory for subsequent rounds of inference", + "help_text": "Type: `integer`, multiple: `False`, example: `2000000`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/common input options" + }, + { + "$ref": "#/$defs/mapping input options" + }, + { + "$ref": "#/$defs/alignment input options" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/basic options" + }, + { + "$ref": "#/$defs/options specific to mapping mode" + }, + { + "$ref": "#/$defs/advance options" + }, + { + "$ref": "#/$defs/alignment-specific options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index bf213685..94e0ab96 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -267,9 +262,9 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -294,6 +289,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index f8b51071..cbcccc2e 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3370,9 +3362,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3388,6 +3380,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_collate/nextflow_schema.json b/target/nextflow/samtools/samtools_collate/nextflow_schema.json index c50e595c..1f22298f 100644 --- a/target/nextflow/samtools/samtools_collate/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_collate/nextflow_schema.json @@ -1,225 +1,131 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_collate", -"description": "Shuffles and groups reads in SAM/BAM/CRAM files together by their names.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. The input BAM file", - "help_text": "Type: `file`, required. The input BAM file." - - } - - - , - "reference": { - "type": - "string", - "description": "Type: `file`. Reference sequence FASTA FILE", - "help_text": "Type: `file`. Reference sequence FASTA FILE." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. The output filename", - "help_text": "Type: `file`, required, default: `$id.$key.output`. The output filename." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "uncompressed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output uncompressed BAM", - "help_text": "Type: `boolean_true`, default: `false`. Output uncompressed BAM." - , - "default":false - } - - - , - "fast": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Fast mode, only primary alignments", - "help_text": "Type: `boolean_true`, default: `false`. Fast mode, only primary alignments." - , - "default":false - } - - - , - "working_reads": { - "type": - "integer", - "description": "Type: `integer`, default: `10000`. Working reads stored (for use with -f)", - "help_text": "Type: `integer`, default: `10000`. Working reads stored (for use with -f)." - , - "default":10000 - } - - - , - "compression": { - "type": - "integer", - "description": "Type: `integer`, default: `1`. Compression level", - "help_text": "Type: `integer`, default: `1`. Compression level." - , - "default":1 - } - - - , - "nb_tmp_files": { - "type": - "integer", - "description": "Type: `integer`, default: `64`. Number of temporary files", - "help_text": "Type: `integer`, default: `64`. Number of temporary files." - , - "default":64 - } - - - , - "tmp_prefix": { - "type": - "string", - "description": "Type: `string`. Write temporary files to PREFIX", - "help_text": "Type: `string`. Write temporary files to PREFIX.nnnn.bam." - - } - - - , - "no_pg": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not add a PG line", - "help_text": "Type: `boolean_true`, default: `false`. Do not add a PG line." - , - "default":false - } - - - , - "input_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE." - - } - - - , - "output_fmt": { - "type": - "string", - "description": "Type: `string`. Specify output format (SAM, BAM, CRAM)", - "help_text": "Type: `string`. Specify output format (SAM, BAM, CRAM)." - - } - - - , - "output_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single output file format option in the form of OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single output file format option in the form of OPTION or OPTION=VALUE." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_collate", + "description": "Shuffles and groups reads in SAM/BAM/CRAM files together by their names.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "The input BAM file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "reference": { + "type": "string", + "format": "path", + "description": "Reference sequence FASTA FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output filename.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "uncompressed": { + "type": "boolean", + "description": "Output uncompressed BAM.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fast": { + "type": "boolean", + "description": "Fast mode, only primary alignments.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "working_reads": { + "type": "integer", + "description": "Working reads stored (for use with -f).", + "help_text": "Type: `integer`, multiple: `False`, default: `10000`. ", + "default": 10000 + }, + "compression": { + "type": "integer", + "description": "Compression level.", + "help_text": "Type: `integer`, multiple: `False`, default: `1`. ", + "default": 1 + }, + "nb_tmp_files": { + "type": "integer", + "description": "Number of temporary files.", + "help_text": "Type: `integer`, multiple: `False`, default: `64`. ", + "default": 64 + }, + "tmp_prefix": { + "type": "string", + "description": "Write temporary files to PREFIX.nnnn.bam.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_pg": { + "type": "boolean", + "description": "Do not add a PG line.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input_fmt_option": { + "type": "string", + "description": "Specify a single input file format option in the form of OPTION or OPTION=VALUE.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "output_fmt": { + "type": "string", + "description": "Specify output format (SAM, BAM, CRAM).", + "help_text": "Type: `string`, multiple: `False`. " + }, + "output_fmt_option": { + "type": "string", + "description": "Specify a single output file format option in the form of OPTION or OPTION=VALUE.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index a76567fe..2ffc30c2 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -246,9 +241,9 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -273,6 +268,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index 2d0dc44d..2913c8d9 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3342,9 +3334,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3360,6 +3352,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_faidx/nextflow_schema.json b/target/nextflow/samtools/samtools_faidx/nextflow_schema.json index 393a3f97..dcecf111 100644 --- a/target/nextflow/samtools/samtools_faidx/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_faidx/nextflow_schema.json @@ -1,196 +1,118 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_faidx", -"description": "Indexes FASTA files to enable random access to fasta and fastq files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`. FASTA input file", - "help_text": "Type: `file`. FASTA input file.\n" - - } - - - , - "length": { - "type": - "integer", - "description": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping", - "help_text": "Type: `integer`, default: `60`. Length for FASTA sequence line wrapping. If zero, this means do not\nline wrap. Defaults to the line length in the input file.\n" - , - "default":60 - } - - - , - "region_file": { - "type": - "string", - "description": "Type: `file`. File of regions", - "help_text": "Type: `file`. File of regions. Format is chr:from-to. One per line.\nMust be used with --output to avoid sending output to stdout.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file", - "help_text": "Type: `file`, required, default: `$id.$key.output.fasta`, example: `output.fasta`. Write output to file.\n" - , - "default":"$id.$key.output.fasta" - } - - - , - "mark_strand": { - "type": - "string", - "description": "Type: `string`, default: `rc`. Add strand indicator to sequence name", - "help_text": "Type: `string`, default: `rc`. Add strand indicator to sequence name. Options are:\n[ rc, no, sign, custom,\u003cpos\u003e,\u003cneg\u003e ]\n" - , - "default":"rc" - } - - - , - "fai_idx": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file", - "help_text": "Type: `file`, default: `$id.$key.fai_idx.fai`, example: `file.fa.fai`. Read/Write to specified index file (default file.fa.fai).\n" - , - "default":"$id.$key.fai_idx.fai" - } - - - , - "gzi_idx": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with ", - "help_text": "Type: `file`, default: `$id.$key.gzi_idx.gzi`, example: `file.fa.gz.gzi`. Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n" - , - "default":"$id.$key.gzi_idx.gzi" - } - - - , - "fastq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format", - "help_text": "Type: `boolean_true`, default: `false`. Read FASTQ files and output extracted sequences in FASTQ format. Same as using samtools fqidx.\n" - , - "default":false - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "continue": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested", - "help_text": "Type: `boolean_true`, default: `false`. Continue working if a non-existent region is requested.\n" - , - "default":false - } - - - , - "reverse_complement": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Reverse complement sequences", - "help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_faidx", + "description": "Indexes FASTA files to enable random access to fasta and fastq files.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "description": "FASTA input file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "length": { + "type": "integer", + "description": "Length for FASTA sequence line wrapping", + "help_text": "Type: `integer`, multiple: `False`, default: `60`. ", + "default": 60 + }, + "region_file": { + "type": "string", + "format": "path", + "description": "File of regions", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Write output to file.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.fasta\"`, direction: `output`, example: `\"output.fasta\"`. ", + "default": "$id.$key.output.fasta" + }, + "mark_strand": { + "type": "string", + "description": "Add strand indicator to sequence name", + "help_text": "Type: `string`, multiple: `False`, default: `\"rc\"`. ", + "default": "rc" + }, + "fai_idx": { + "type": "string", + "format": "path", + "description": "Read/Write to specified index file (default file.fa.fai).\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fai_idx.fai\"`, direction: `output`, example: `\"file.fa.fai\"`. ", + "default": "$id.$key.fai_idx.fai" + }, + "gzi_idx": { + "type": "string", + "format": "path", + "description": "Read/Write to specified compressed file index (used with .gz files, default file.fa.gz.gzi).\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.gzi_idx.gzi\"`, direction: `output`, example: `\"file.fa.gz.gzi\"`. ", + "default": "$id.$key.gzi_idx.gzi" + }, + "fastq": { + "type": "boolean", + "description": "Read FASTQ files and output extracted sequences in FASTQ format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "continue": { + "type": "boolean", + "description": "Continue working if a non-existent region is requested.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "reverse_complement": { + "type": "boolean", + "description": "Reverse complement sequences.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 90181320..65fcefb5 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -436,9 +431,9 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -463,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index 4f57e1c0..58c1b655 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3534,9 +3526,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3552,6 +3544,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json index f7a9a5dc..c95edd4c 100644 --- a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json @@ -1,348 +1,200 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_fasta", -"description": "Converts a SAM, BAM or CRAM to FASTA format.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. input SAM/BAM/CRAM file", - "help_text": "Type: `file`, required. input SAM/BAM/CRAM file" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. output FASTA file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. output FASTA file" - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "no_suffix": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", - "help_text": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.\n" - , - "default":false - } - - - , - "suffix": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files", - "help_text": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files.\n" - , - "default":false - } - - - , - "use_oq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available", - "help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n" - , - "default":false - } - - - , - "singleton": { - "type": - "string", - "description": "Type: `file`. write singleton reads to FILE", - "help_text": "Type: `file`. write singleton reads to FILE." - - } - - - , - "copy_tags": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTA header line, if they exist", - "help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTA header line, if they exist.\n" - , - "default":false - } - - - , - "copy_tags_list": { - "type": - "string", - "description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTA header line, if they exist", - "help_text": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTA header line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted shell expansion.\n" - - } - - - , - "read1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" - , - "default":"$id.$key.read1" - } - - - , - "read2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" - , - "default":"$id.$key.read2" - } - - - , - "output_reads": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", - "help_text": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" - , - "default":"$id.$key.output_reads" - } - - - , - "output_reads_both": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" - , - "default":"$id.$key.output_reads_both" - } - - - , - "filter_flags": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field", - "help_text": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 \n(i.e. /^0[0-7]+/). Default: `0`.\n" - - } - - - , - "excl_flags": { - "type": - "string", - "description": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field", - "help_text": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and \nsupplementary alignments. Default: `0x900`.\n" - - } - - - , - "incl_flags": { - "type": - "string", - "description": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field", - "help_text": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of \nflag names. Default: `0`.\n" - - } - - - , - "excl_flags_all": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", - "help_text": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 (i.e. /^0[0-7]+/).\nDefault: `0`.\n" - - } - - - , - "aux_tag": { - "type": - "string", - "description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL", - "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is comparable to the method used in samtools view --tag. The option may be specified \nmultiple times and is equivalent to using the --aux_tag_file option.\n" - - } - - - , - "aux_tag_file": { - "type": - "string", - "description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", - "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. \nThe format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.\n" - - } - - - , - "casava": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. add Illumina Casava 1", - "help_text": "Type: `boolean_true`, default: `false`. add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)" - , - "default":false - } - - - , - "compression": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fasta files", - "help_text": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fasta files." - - } - - - , - "index1": { - "type": - "string", - "description": "Type: `file`. write first index reads to FILE", - "help_text": "Type: `file`. write first index reads to FILE." - - } - - - , - "index2": { - "type": - "string", - "description": "Type: `file`. write second index reads to FILE", - "help_text": "Type: `file`. write second index reads to FILE." - - } - - - , - "barcode_tag": { - "type": - "string", - "description": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in", - "help_text": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in. Default: `BC`.\n" - - } - - - , - "quality_tag": { - "type": - "string", - "description": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in", - "help_text": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in. Default: `QT`.\n" - - } - - - , - "index_format": { - "type": - "string", - "description": "Type: `string`. string to describe how to parse the barcode and quality tags", - "help_text": "Type: `string`. string to describe how to parse the barcode and quality tags. For example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.\nIf the tag contains a separator, then the numeric part can be replaced with`*` to mean \n\u0027read until the separator or end of tag\u0027, for example: `n*i*`.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_fasta", + "description": "Converts a SAM, BAM or CRAM to FASTA format.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "input SAM/BAM/CRAM file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "output FASTA file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "no_suffix": { + "type": "boolean", + "description": "By default, either '/1' or '/2' is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "suffix": { + "type": "boolean", + "description": "Always add either '/1' or '/2' to the end of read names even when put into different files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "use_oq": { + "type": "boolean", + "description": "Use quality values from OQ tags in preference to standard quality string if available.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "singleton": { + "type": "string", + "format": "path", + "description": "write singleton reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "copy_tags": { + "type": "boolean", + "description": "Copy RG, BC and QT tags to the FASTA header line, if they exist.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "copy_tags_list": { + "type": "string", + "description": "Specify a comma-separated list of tags to copy to the FASTA header line, if they exist", + "help_text": "Type: `string`, multiple: `False`. " + }, + "read1": { + "type": "string", + "format": "path", + "description": "Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.read1\"`, direction: `output`. ", + "default": "$id.$key.read1" + }, + "read2": { + "type": "string", + "format": "path", + "description": "Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.read2\"`, direction: `output`. ", + "default": "$id.$key.read2" + }, + "output_reads": { + "type": "string", + "format": "path", + "description": "Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_reads\"`, direction: `output`. ", + "default": "$id.$key.output_reads" + }, + "output_reads_both": { + "type": "string", + "format": "path", + "description": "Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_reads_both\"`, direction: `output`. ", + "default": "$id.$key.output_reads_both" + }, + "filter_flags": { + "type": "integer", + "description": "Only output alignments with all bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "excl_flags": { + "type": "string", + "description": "Do not output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`, example: `\"0x900\"`. " + }, + "incl_flags": { + "type": "string", + "description": "Only output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. " + }, + "excl_flags_all": { + "type": "integer", + "description": "Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "aux_tag": { + "type": "string", + "description": "Only output alignments containing an auxiliary tag matching both TAG and VAL", + "help_text": "Type: `string`, multiple: `False`. " + }, + "aux_tag_file": { + "type": "string", + "description": "Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", + "help_text": "Type: `string`, multiple: `False`. " + }, + "casava": { + "type": "boolean", + "description": "add Illumina Casava 1.8 format entry to header (eg 1:N:0:ATCACG)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "compression": { + "type": "integer", + "description": "set compression level when writing gz or bgzf fasta files.", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "index1": { + "type": "string", + "format": "path", + "description": "write first index reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "index2": { + "type": "string", + "format": "path", + "description": "write second index reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "barcode_tag": { + "type": "string", + "description": "Auxiliary tag to find index reads in", + "help_text": "Type: `string`, multiple: `False`, example: `\"BC\"`. " + }, + "quality_tag": { + "type": "string", + "description": "Auxiliary tag to find index quality in", + "help_text": "Type: `string`, multiple: `False`, example: `\"QT\"`. " + }, + "index_format": { + "type": "string", + "description": "string to describe how to parse the barcode and quality tags", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 04c88fca..43725ffb 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -436,9 +431,9 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -463,6 +458,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index a51cf075..42a3143d 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3534,9 +3526,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3552,6 +3544,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json index 98acdf76..4c3caf29 100644 --- a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json @@ -1,348 +1,200 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_fastq", -"description": "Converts a SAM, BAM or CRAM to FASTQ format.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. input SAM/BAM/CRAM file", - "help_text": "Type: `file`, required. input SAM/BAM/CRAM file" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. output FASTQ file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. output FASTQ file" - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "no_suffix": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", - "help_text": "Type: `boolean_true`, default: `false`. By default, either \u0027/1\u0027 or \u0027/2\u0027 is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.\n" - , - "default":false - } - - - , - "suffix": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files", - "help_text": "Type: `boolean_true`, default: `false`. Always add either \u0027/1\u0027 or \u0027/2\u0027 to the end of read names even when put into different files.\n" - , - "default":false - } - - - , - "use_oq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available", - "help_text": "Type: `boolean_true`, default: `false`. Use quality values from OQ tags in preference to standard quality string if available.\n" - , - "default":false - } - - - , - "singleton": { - "type": - "string", - "description": "Type: `file`. write singleton reads to FILE", - "help_text": "Type: `file`. write singleton reads to FILE." - - } - - - , - "copy_tags": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist", - "help_text": "Type: `boolean_true`, default: `false`. Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n" - , - "default":false - } - - - , - "copy_tags_list": { - "type": - "string", - "description": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist", - "help_text": "Type: `string`. Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist. \nTAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`, \nbe careful to quote it to avoid unwanted shell expansion.\n" - - } - - - , - "read1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read1`. Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" - , - "default":"$id.$key.read1" - } - - - , - "read2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.read2`. Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them. \nIf the -s option is used, only paired reads will be written to this file.\n" - , - "default":"$id.$key.read2" - } - - - , - "output_reads": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", - "help_text": "Type: `file`, default: `$id.$key.output_reads`. Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout. \nThis is equivalent to -1 FILE -2 FILE.\n" - , - "default":"$id.$key.output_reads" - } - - - , - "output_reads_both": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them", - "help_text": "Type: `file`, default: `$id.$key.output_reads_both`. Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n" - , - "default":"$id.$key.output_reads_both" - } - - - , - "filter_flags": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field", - "help_text": "Type: `integer`, example: `0`. Only output alignments with all bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/). Default: `0`.\n" - - } - - - , - "excl_flags": { - "type": - "string", - "description": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field", - "help_text": "Type: `string`, example: `0x900`. Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 \n(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and \nsupplementary alignments. Default: `0x900`.\n" - - } - - - , - "incl_flags": { - "type": - "string", - "description": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field", - "help_text": "Type: `string`, example: `0`. Only output alignments with any bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with \u00270\u0027\n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of \nflag names. Default: `0`.\n" - - } - - - , - "excl_flags_all": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", - "help_text": "Type: `integer`, example: `0`. Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified \nin hex by beginning with \u00270x\u0027 (i.e. /^0x[0-9A-F]+/) or in octal by beginning with \u00270\u0027 (i.e. /^0[0-7]+/).\nDefault: `0`.\n" - - } - - - , - "aux_tag": { - "type": - "string", - "description": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL", - "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted \nthen any value is accepted. The tag types supported are i, f, Z, A and H. \"B\" arrays are not \nsupported. This is comparable to the method used in samtools view --tag. The option may be specified \nmultiple times and is equivalent to using the --aux_tag_file option.\n" - - } - - - , - "aux_tag_file": { - "type": - "string", - "description": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", - "help_text": "Type: `string`. Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE. \nThe format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.\n" - - } - - - , - "casava": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add Illumina Casava 1", - "help_text": "Type: `boolean_true`, default: `false`. Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.\n" - , - "default":false - } - - - , - "compression": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fastq files", - "help_text": "Type: `integer`, example: `0`. set compression level when writing gz or bgzf fastq files." - - } - - - , - "index1": { - "type": - "string", - "description": "Type: `file`. write first index reads to FILE", - "help_text": "Type: `file`. write first index reads to FILE." - - } - - - , - "index2": { - "type": - "string", - "description": "Type: `file`. write second index reads to FILE", - "help_text": "Type: `file`. write second index reads to FILE." - - } - - - , - "barcode_tag": { - "type": - "string", - "description": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in", - "help_text": "Type: `string`, example: `BC`. Auxiliary tag to find index reads in. Default: `BC`.\n" - - } - - - , - "quality_tag": { - "type": - "string", - "description": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in", - "help_text": "Type: `string`, example: `QT`. Auxiliary tag to find index quality in. Default: `QT`.\n" - - } - - - , - "index_format": { - "type": - "string", - "description": "Type: `string`. string to describe how to parse the barcode and quality tags", - "help_text": "Type: `string`. string to describe how to parse the barcode and quality tags. For example:\n* `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.\n* `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.\nIf the tag contains a separator, then the numeric part can be replaced with \u0027*\u0027 to mean \n\u0027read until the separator or end of tag\u0027, for example: `n*i*`.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_fastq", + "description": "Converts a SAM, BAM or CRAM to FASTQ format.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "input SAM/BAM/CRAM file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "output FASTQ file", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "no_suffix": { + "type": "boolean", + "description": "By default, either '/1' or '/2' is added to the end of read names where the corresponding \nREAD1 or READ2 FLAG bit is set", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "suffix": { + "type": "boolean", + "description": "Always add either '/1' or '/2' to the end of read names even when put into different files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "use_oq": { + "type": "boolean", + "description": "Use quality values from OQ tags in preference to standard quality string if available.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "singleton": { + "type": "string", + "format": "path", + "description": "write singleton reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "copy_tags": { + "type": "boolean", + "description": "Copy RG, BC and QT tags to the FASTQ header line, if they exist.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "copy_tags_list": { + "type": "string", + "description": "Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist", + "help_text": "Type: `string`, multiple: `False`. " + }, + "read1": { + "type": "string", + "format": "path", + "description": "Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.read1\"`, direction: `output`. ", + "default": "$id.$key.read1" + }, + "read2": { + "type": "string", + "format": "path", + "description": "Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.read2\"`, direction: `output`. ", + "default": "$id.$key.read2" + }, + "output_reads": { + "type": "string", + "format": "path", + "description": "Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_reads\"`, direction: `output`. ", + "default": "$id.$key.output_reads" + }, + "output_reads_both": { + "type": "string", + "format": "path", + "description": "Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE \ninstead of outputting them.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_reads_both\"`, direction: `output`. ", + "default": "$id.$key.output_reads_both" + }, + "filter_flags": { + "type": "integer", + "description": "Only output alignments with all bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "excl_flags": { + "type": "string", + "description": "Do not output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`, example: `\"0x900\"`. " + }, + "incl_flags": { + "type": "string", + "description": "Only output alignments with any bits set in INT present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. " + }, + "excl_flags_all": { + "type": "integer", + "description": "Only EXCLUDE reads with all of the bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "aux_tag": { + "type": "string", + "description": "Only output alignments containing an auxiliary tag matching both TAG and VAL", + "help_text": "Type: `string`, multiple: `False`. " + }, + "aux_tag_file": { + "type": "string", + "description": "Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE", + "help_text": "Type: `string`, multiple: `False`. " + }, + "casava": { + "type": "boolean", + "description": "Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "compression": { + "type": "integer", + "description": "set compression level when writing gz or bgzf fastq files.", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "index1": { + "type": "string", + "format": "path", + "description": "write first index reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "index2": { + "type": "string", + "format": "path", + "description": "write second index reads to FILE.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "barcode_tag": { + "type": "string", + "description": "Auxiliary tag to find index reads in", + "help_text": "Type: `string`, multiple: `False`, example: `\"BC\"`. " + }, + "quality_tag": { + "type": "string", + "description": "Auxiliary tag to find index quality in", + "help_text": "Type: `string`, multiple: `False`, example: `\"QT\"`. " + }, + "index_format": { + "type": "string", + "description": "string to describe how to parse the barcode and quality tags", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index e4ed03b9..0c83e4ce 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -176,9 +171,9 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -203,6 +198,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index 058eb05a..1c92cd3e 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3258,9 +3250,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3276,6 +3268,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json b/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json index 77d8de7e..b52c82a2 100644 --- a/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json @@ -1,105 +1,64 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_flagstat", -"description": "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "bam": { - "type": - "string", - "description": "Type: `file`. BAM input files", - "help_text": "Type: `file`. BAM input files.\n" - - } - - - , - "bai": { - "type": - "string", - "description": "Type: `file`. BAM index file", - "help_text": "Type: `file`. BAM index file.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output", - "help_text": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output.\n" - , - "default":"$id.$key.output.flagstat" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_flagstat", + "description": "Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "bam": { + "type": "string", + "format": "path", + "description": "BAM input files.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "bai": { + "type": "string", + "format": "path", + "description": "BAM index file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "File containing samtools stats output.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.flagstat\"`, direction: `output`, example: `\"output.flagstat\"`. ", + "default": "$id.$key.output.flagstat" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index cd4bd8a6..c5229811 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -186,9 +181,9 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -213,6 +208,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 02b55e5c..c8cdc07d 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3270,9 +3262,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3288,6 +3280,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json b/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json index 3b43ccc8..ec0a1949 100644 --- a/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json @@ -1,115 +1,70 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_idxstats", -"description": "Reports alignment summary statistics for a BAM file.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "bam": { - "type": - "string", - "description": "Type: `file`. BAM input file", - "help_text": "Type: `file`. BAM input file." - - } - - - , - "bai": { - "type": - "string", - "description": "Type: `file`. BAM index file", - "help_text": "Type: `file`. BAM index file." - - } - - - , - "fasta": { - "type": - "string", - "description": "Type: `file`. Reference file the CRAM was created with (optional)", - "help_text": "Type: `file`. Reference file the CRAM was created with (optional)." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format", - "help_text": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format.\n" - , - "default":"$id.$key.output.idxstats" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_idxstats", + "description": "Reports alignment summary statistics for a BAM file.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "bam": { + "type": "string", + "format": "path", + "description": "BAM input file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "bai": { + "type": "string", + "format": "path", + "description": "BAM index file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "fasta": { + "type": "string", + "format": "path", + "description": "Reference file the CRAM was created with (optional).", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "File containing samtools stats output in tab-delimited format.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.idxstats\"`, direction: `output`, example: `\"output.idxstats\"`. ", + "default": "$id.$key.output.idxstats" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index ed51e714..f007a20b 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -192,9 +187,9 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -219,6 +214,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index 86d0b506..995eb8a5 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3283,9 +3275,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3301,6 +3293,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_index/nextflow_schema.json b/target/nextflow/samtools/samtools_index/nextflow_schema.json index 1617235c..58aded95 100644 --- a/target/nextflow/samtools/samtools_index/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_index/nextflow_schema.json @@ -1,141 +1,86 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_index", -"description": "Index SAM/BAM/CRAM files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file name", - "help_text": "Type: `file`, required. Input file name" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name", - "help_text": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name" - , - "default":"$id.$key.output.bai" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "bai": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Generate BAM index", - "help_text": "Type: `boolean_true`, default: `false`. Generate BAM index" - , - "default":false - } - - - , - "csi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex", - "help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex. This will be required for genomes with larger chromosome \nsizes.\n" - , - "default":false - } - - - , - "min_shift": { - "type": - "integer", - "description": "Type: `integer`. Create a CSI index, with a minimum interval size of 2^INT", - "help_text": "Type: `integer`. Create a CSI index, with a minimum interval size of 2^INT.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_index", + "description": "Index SAM/BAM/CRAM files.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file name", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file name", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bai\"`, direction: `output`, example: `\"out.bam.bai\"`. ", + "default": "$id.$key.output.bai" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "bai": { + "type": "boolean", + "description": "Generate BAM index", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "csi": { + "type": "boolean", + "description": "Create a CSI index for BAM files instead of the traditional BAI \nindex", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "min_shift": { + "type": "integer", + "description": "Create a CSI index, with a minimum interval size of 2^INT.\n", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 8ec494b6..d272267f 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -335,9 +330,9 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -362,6 +357,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index fdd0c0e0..670d76eb 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3455,9 +3447,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3473,6 +3465,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_sort/nextflow_schema.json b/target/nextflow/samtools/samtools_sort/nextflow_schema.json index b46fa994..1f71f931 100644 --- a/target/nextflow/samtools/samtools_sort/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_sort/nextflow_schema.json @@ -1,309 +1,176 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_sort", -"description": "Sort SAM/BAM/CRAM file.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. SAM/BAM/CRAM input file", - "help_text": "Type: `file`, required. SAM/BAM/CRAM input file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file", - "help_text": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file.\n" - , - "default":"$id.$key.output.bam" - } - - - , - "output_fmt": { - "type": - "string", - "description": "Type: `string`, example: `BAM`. Specify output format (SAM, BAM, CRAM)", - "help_text": "Type: `string`, example: `BAM`. Specify output format (SAM, BAM, CRAM).\n" - - } - - - , - "output_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single output file format option in the form\nof OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single output file format option in the form\nof OPTION or OPTION=VALUE.\n" - - } - - - , - "reference": { - "type": - "string", - "description": "Type: `file`, example: `ref.fa`. Reference sequence FASTA FILE", - "help_text": "Type: `file`, example: `ref.fa`. Reference sequence FASTA FILE.\n" - - } - - - , - "write_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Automatically index the output files", - "help_text": "Type: `boolean_true`, default: `false`. Automatically index the output files.\n" - , - "default":false - } - - - , - "prefix": { - "type": - "string", - "description": "Type: `string`. Write temporary files to PREFIX", - "help_text": "Type: `string`. Write temporary files to PREFIX.nnnn.bam.\n" - - } - - - , - "no_PG": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not add a PG line", - "help_text": "Type: `boolean_true`, default: `false`. Do not add a PG line.\n" - , - "default":false - } - - - , - "template_coordinate": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by template-coordinate", - "help_text": "Type: `boolean_true`, default: `false`. Sort by template-coordinate.\n" - , - "default":false - } - - - , - "input_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single input file format option in the form\nof OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single input file format option in the form\nof OPTION or OPTION=VALUE.\n" - - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "compression": { - "type": - "integer", - "description": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best)", - "help_text": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best).\n" - , - "default":0 - } - - - , - "uncompressed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0)", - "help_text": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0).\n" - , - "default":false - } - - - , - "minimiser": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads", - "help_text": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads.\n" - , - "default":false - } - - - , - "not_reverse": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n", - "help_text": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n" - , - "default":false - } - - - , - "kmer_size": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. Kmer size to use for minimiser", - "help_text": "Type: `integer`, example: `20`. Kmer size to use for minimiser.\n" - - } - - - , - "order": { - "type": - "string", - "description": "Type: `file`, example: `ref.fa`. Order minimisers by their position in FILE FASTA", - "help_text": "Type: `file`, example: `ref.fa`. Order minimisers by their position in FILE FASTA.\n" - - } - - - , - "window": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. Window size for minimiser INDEXING VIA --order REF", - "help_text": "Type: `integer`, example: `100`. Window size for minimiser INDEXING VIA --order REF.FA.\n" - - } - - - , - "homopolymers": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser", - "help_text": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser.\n" - , - "default":false - } - - - , - "natural_sort": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index", - "help_text": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index.\n" - , - "default":false - } - - - , - "ascii_sort": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index", - "help_text": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index.\n" - , - "default":false - } - - - , - "tag": { - "type": - "string", - "description": "Type: `string`. Sort by value of TAG", - "help_text": "Type: `string`. Sort by value of TAG. Uses position as secondary index \n(or read name if --natural_sort is set).\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_sort", + "description": "Sort SAM/BAM/CRAM file.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "SAM/BAM/CRAM input file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Write final output to file.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"out.bam\"`. ", + "default": "$id.$key.output.bam" + }, + "output_fmt": { + "type": "string", + "description": "Specify output format (SAM, BAM, CRAM).\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"BAM\"`. " + }, + "output_fmt_option": { + "type": "string", + "description": "Specify a single output file format option in the form\nof OPTION or OPTION=VALUE.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "reference": { + "type": "string", + "format": "path", + "description": "Reference sequence FASTA FILE.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"ref.fa\"`. " + }, + "write_index": { + "type": "boolean", + "description": "Automatically index the output files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "prefix": { + "type": "string", + "description": "Write temporary files to PREFIX.nnnn.bam.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_PG": { + "type": "boolean", + "description": "Do not add a PG line.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "template_coordinate": { + "type": "boolean", + "description": "Sort by template-coordinate.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input_fmt_option": { + "type": "string", + "description": "Specify a single input file format option in the form\nof OPTION or OPTION=VALUE.\n", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "compression": { + "type": "integer", + "description": "Set compression level, from 0 (uncompressed) to 9 (best).\n", + "help_text": "Type: `integer`, multiple: `False`, default: `0`. ", + "default": 0 + }, + "uncompressed": { + "type": "boolean", + "description": "Output uncompressed data (equivalent to --compression 0).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "minimiser": { + "type": "boolean", + "description": "Use minimiser for clustering unaligned/unplaced reads.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "not_reverse": { + "type": "boolean", + "description": "Do not use reverse strand (only compatible with --minimiser)\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "kmer_size": { + "type": "integer", + "description": "Kmer size to use for minimiser.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "order": { + "type": "string", + "format": "path", + "description": "Order minimisers by their position in FILE FASTA.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"ref.fa\"`. " + }, + "window": { + "type": "integer", + "description": "Window size for minimiser INDEXING VIA --order REF.FA.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "homopolymers": { + "type": "boolean", + "description": "Squash homopolymers when computing minimiser.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "natural_sort": { + "type": "boolean", + "description": "Sort by read name (natural): cannot be used with samtools index.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ascii_sort": { + "type": "boolean", + "description": "Sort by read name (ASCII): cannot be used with samtools index.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "tag": { + "type": "string", + "description": "Sort by value of TAG", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index 7e0f1429..304c491d 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -404,9 +399,9 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -431,6 +426,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 8e3e926d..f1820d02 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3525,9 +3517,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3543,6 +3535,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_stats/nextflow_schema.json b/target/nextflow/samtools/samtools_stats/nextflow_schema.json index 4e161ad1..50cb3397 100644 --- a/target/nextflow/samtools/samtools_stats/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_stats/nextflow_schema.json @@ -1,319 +1,181 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_stats", -"description": "Reports alignment summary statistics for a BAM file.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input file", - "help_text": "Type: `file`, required. Input file.\n" - - } - - - , - "bai": { - "type": - "string", - "description": "Type: `file`. Index file", - "help_text": "Type: `file`. Index file.\n" - - } - - - , - "fasta": { - "type": - "string", - "description": "Type: `file`. Reference file the CRAM was created with", - "help_text": "Type: `file`. Reference file the CRAM was created with.\n" - - } - - - , - "coverage": { - "type": - "string", - "description": "Type: List of `integer`, example: `1;1000;1`, multiple_sep: `\";\"`. Coverage distribution min;max;step", - "help_text": "Type: List of `integer`, example: `1;1000;1`, multiple_sep: `\";\"`. Coverage distribution min;max;step. Default: [1, 1000, 1].\n" - - } - - - , - "remove_dups": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Exclude from statistics reads marked as duplicates", - "help_text": "Type: `boolean_true`, default: `false`. Exclude from statistics reads marked as duplicates.\n" - , - "default":false - } - - - , - "customized_index_file": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use a customized index file", - "help_text": "Type: `boolean_true`, default: `false`. Use a customized index file.\n" - , - "default":false - } - - - , - "required_flag": { - "type": - "string", - "description": "Type: `string`, example: `0`. Required flag, 0 for unset", - "help_text": "Type: `string`, example: `0`. Required flag, 0 for unset. See also `samtools flags`. Default: `\"0\"`.\n" - - } - - - , - "filtering_flag": { - "type": - "string", - "description": "Type: `string`, example: `0`. Filtering flag, 0 for unset", - "help_text": "Type: `string`, example: `0`. Filtering flag, 0 for unset. See also `samtools flags`. Default: `0`.\n" - - } - - - , - "GC_depth": { - "type": - "number", - "description": "Type: `double`, example: `20000.0`. The size of GC-depth bins (decreasing bin size increases memory requirement)", - "help_text": "Type: `double`, example: `20000.0`. The size of GC-depth bins (decreasing bin size increases memory requirement). Default: `20000`.\n" - - } - - - , - "insert_size": { - "type": - "integer", - "description": "Type: `integer`, example: `8000`. Maximum insert size", - "help_text": "Type: `integer`, example: `8000`. Maximum insert size. Default: `8000`.\n" - - } - - - , - "id": { - "type": - "string", - "description": "Type: `string`. Include only listed read group or sample name", - "help_text": "Type: `string`. Include only listed read group or sample name.\n" - - } - - - , - "read_length": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. Include in the statistics only reads with the given read length", - "help_text": "Type: `integer`, example: `-1`. Include in the statistics only reads with the given read length. Default: `-1`.\n" - - } - - - , - "most_inserts": { - "type": - "number", - "description": "Type: `double`, example: `0.99`. Report only the main part of inserts", - "help_text": "Type: `double`, example: `0.99`. Report only the main part of inserts. Default: `0.99`.\n" - - } - - - , - "split_prefix": { - "type": - "string", - "description": "Type: `string`. Path or string prefix for filepaths output by --split (default is input filename)", - "help_text": "Type: `string`. Path or string prefix for filepaths output by --split (default is input filename).\n" - - } - - - , - "trim_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. The BWA trimming parameter", - "help_text": "Type: `integer`, example: `0`. The BWA trimming parameter. Default: `0`.\n" - - } - - - , - "ref_seq": { - "type": - "string", - "description": "Type: `file`. Reference sequence (required for GC-depth and mismatches-per-cycle calculation)", - "help_text": "Type: `file`. Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n" - - } - - - , - "split": { - "type": - "string", - "description": "Type: `string`. Also write statistics to separate files split by tagged field", - "help_text": "Type: `string`. Also write statistics to separate files split by tagged field.\n" - - } - - - , - "target_regions": { - "type": - "string", - "description": "Type: `file`. Do stats in these regions only", - "help_text": "Type: `file`. Do stats in these regions only. Tab-delimited file chr,from,to, 1-based, inclusive.\n" - - } - - - , - "sparse": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Suppress outputting IS rows where there are no insertions", - "help_text": "Type: `boolean_true`, default: `false`. Suppress outputting IS rows where there are no insertions.\n" - , - "default":false - } - - - , - "remove_overlaps": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Remove overlaps of paired-end reads from coverage and base count computations", - "help_text": "Type: `boolean_true`, default: `false`. Remove overlaps of paired-end reads from coverage and base count computations.\n" - , - "default":false - } - - - , - "cov_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Only bases with coverage above this value will be included in the target percentage computation", - "help_text": "Type: `integer`, example: `0`. Only bases with coverage above this value will be included in the target percentage computation. Default: `0`.\n" - - } - - - , - "input_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE.\n" - - } - - - , - "reference": { - "type": - "string", - "description": "Type: `file`. Reference sequence FASTA FILE", - "help_text": "Type: `file`. Reference sequence FASTA FILE.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `out.txt`. Output file", - "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `out.txt`. Output file.\n" - , - "default":"$id.$key.output.txt" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_stats", + "description": "Reports alignment summary statistics for a BAM file.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input file.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "bai": { + "type": "string", + "format": "path", + "description": "Index file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "fasta": { + "type": "string", + "format": "path", + "description": "Reference file the CRAM was created with.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "coverage": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Coverage distribution min;max;step", + "help_text": "Type: `integer`, multiple: `True`, example: `[1;1000;1]`. " + }, + "remove_dups": { + "type": "boolean", + "description": "Exclude from statistics reads marked as duplicates.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "customized_index_file": { + "type": "boolean", + "description": "Use a customized index file.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "required_flag": { + "type": "string", + "description": "Required flag, 0 for unset", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. " + }, + "filtering_flag": { + "type": "string", + "description": "Filtering flag, 0 for unset", + "help_text": "Type: `string`, multiple: `False`, example: `\"0\"`. " + }, + "GC_depth": { + "type": "number", + "description": "The size of GC-depth bins (decreasing bin size increases memory requirement)", + "help_text": "Type: `double`, multiple: `False`, example: `20000.0`. " + }, + "insert_size": { + "type": "integer", + "description": "Maximum insert size", + "help_text": "Type: `integer`, multiple: `False`, example: `8000`. " + }, + "id": { + "type": "string", + "description": "Include only listed read group or sample name.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "read_length": { + "type": "integer", + "description": "Include in the statistics only reads with the given read length", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "most_inserts": { + "type": "number", + "description": "Report only the main part of inserts", + "help_text": "Type: `double`, multiple: `False`, example: `0.99`. " + }, + "split_prefix": { + "type": "string", + "description": "Path or string prefix for filepaths output by --split (default is input filename).\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "trim_quality": { + "type": "integer", + "description": "The BWA trimming parameter", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "ref_seq": { + "type": "string", + "format": "path", + "description": "Reference sequence (required for GC-depth and mismatches-per-cycle calculation).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "split": { + "type": "string", + "description": "Also write statistics to separate files split by tagged field.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "target_regions": { + "type": "string", + "format": "path", + "description": "Do stats in these regions only", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "sparse": { + "type": "boolean", + "description": "Suppress outputting IS rows where there are no insertions.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "remove_overlaps": { + "type": "boolean", + "description": "Remove overlaps of paired-end reads from coverage and base count computations.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "cov_threshold": { + "type": "integer", + "description": "Only bases with coverage above this value will be included in the target percentage computation", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "input_fmt_option": { + "type": "string", + "description": "Specify a single input file format option in the form of OPTION or OPTION=VALUE.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "reference": { + "type": "string", + "format": "path", + "description": "Reference sequence FASTA FILE.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file.\n", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"out.txt\"`. ", + "default": "$id.$key.output.txt" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index 0579a491..f405129f 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -668,9 +663,9 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -695,6 +690,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index 12eaae83..051c0760 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3706,9 +3698,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3724,6 +3716,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/samtools/samtools_view/nextflow_schema.json b/target/nextflow/samtools/samtools_view/nextflow_schema.json index ef26805a..6b10fa93 100644 --- a/target/nextflow/samtools/samtools_view/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_view/nextflow_schema.json @@ -1,543 +1,300 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "samtools_view", -"description": "Views and converts SAM/BAM/CRAM files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input SAM, BAM, or CRAM file", - "help_text": "Type: `file`, required. Input SAM, BAM, or CRAM file." - - } - - - , - "fai_reference": { - "type": - "string", - "description": "Type: `file`. A tab-delimited FILE", - "help_text": "Type: `file`. A tab-delimited FILE. Each line must contain the reference name in the first column\nand the length of the reference in the second column, with one line for each distinct\nreference. Any additional fields beyond the second column are ignored. This file also\ndefines the order of the reference sequences in sorting. If you run: `samtools faidx \u003cref.fa\u003e\u0027,\nthe resulting index file \u003cref.fa\u003e.fai can be used as this FILE.\n" - - } - - - , - "reference": { - "type": - "string", - "description": "Type: `file`. A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools faidx", - "help_text": "Type: `file`. A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools faidx.\nIf an index is not present one will be generated for you, if the reference file is local.\nIf the reference file is not local, but is accessed instead via an https://, s3:// or other URL,\nthe index file will need to be supplied by the server alongside the reference. It is possible to\nhave the reference and index files in different locations by supplying both to this option separated\nby the string \"##idx##\", for example:\n--reference ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai\nHowever, note that only the location of the reference will be stored in the output file header.\nIf this method is used to make CRAM files, the cram reader may not be able to find the index,\nand may not be able to decode the file unless it can get the references it needs using a different\nmethod.\n" - - } - - - , - "target_file": { - "type": - "string", - "description": "Type: `file`. Only output alignments overlapping the input BED FILE [null]", - "help_text": "Type: `file`. Only output alignments overlapping the input BED FILE [null].\n" - - } - - - , - "region_file": { - "type": - "string", - "description": "Type: `file`. Use an index and multi-region iterator to only output alignments overlapping the input BED FILE", - "help_text": "Type: `file`. Use an index and multi-region iterator to only output alignments overlapping the input BED FILE.\nEquivalent to --use_index --target_file FILE.\n" - - } - - - , - "qname_file": { - "type": - "string", - "description": "Type: `file`. Output only alignments with read names listed in FILE", - "help_text": "Type: `file`. Output only alignments with read names listed in FILE. If FILE starts with ^ then the operation is\nnegated and only outputs alignment with read groups not listed in FILE. It is not permissible to mix\nboth the filter-in and filter-out style syntax in the same command.\n" - - } - - - , - "read_group_file": { - "type": - "string", - "description": "Type: `file`. Output alignments in read groups listed in FILE [null]", - "help_text": "Type: `file`. Output alignments in read groups listed in FILE [null]. If FILE starts with ^ then the operation is\nnegated and only outputs alignment with read names not listed in FILE. It is not permissible to mix\nboth the filter-in and filter-out style syntax in the same command. Note that records with no RG tag\nwill also be output when using this option. This behaviour may change in a future release.\n" - - } - - - , - "use_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the multi-region iterator on the union of a BED file and command-line region arguments", - "help_text": "Type: `boolean_true`, default: `false`. Use the multi-region iterator on the union of a BED file and command-line region arguments.\nThis avoids re-reading the same regions of files so can sometimes be much faster. Note this also\nremoves duplicate sequences. Without this a sequence that overlaps multiple regions specified on\nthe command line will be reported multiple times. The usage of a BED file is optional and its path\nhas to be preceded by --target_file option.\n" - , - "default":false - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.bam`, example: `output.bam`. Output to FILE instead of [stdout]", - "help_text": "Type: `file`, required, default: `$id.$key.output.bam`, example: `output.bam`. Output to FILE instead of [stdout]." - , - "default":"$id.$key.output.bam" - } - - - , - "bam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output in the BAM format", - "help_text": "Type: `boolean_true`, default: `false`. Output in the BAM format." - , - "default":false - } - - - , - "cram": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output in the CRAM format (requires --reference)", - "help_text": "Type: `boolean_true`, default: `false`. Output in the CRAM format (requires --reference).\n" - , - "default":false - } - - - , - "fast": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Enable fast compression", - "help_text": "Type: `boolean_true`, default: `false`. Enable fast compression. This also changes the default output format to BAM,\nbut this can be overridden by the explicit format options or using a filename\nwith a known suffix.\n" - , - "default":false - } - - - , - "uncompressed": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output uncompressed data", - "help_text": "Type: `boolean_true`, default: `false`. Output uncompressed data. This also changes the default output format to BAM,\nbut this can be overridden by the explicit format options or using a filename\nwith a known suffix.\nThis option saves time spent on compression/decompression and is thus preferred\nwhen the output is piped to another samtools command.\n" - , - "default":false - } - - - , - "with_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Include the header in the output", - "help_text": "Type: `boolean_true`, default: `false`. Include the header in the output.\n" - , - "default":false - } - - - , - "header_only": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output the header only", - "help_text": "Type: `boolean_true`, default: `false`. Output the header only.\n" - , - "default":false - } - - - , - "no_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. When producing SAM format, output alignment records but not headers", - "help_text": "Type: `boolean_true`, default: `false`. When producing SAM format, output alignment records but not headers.\nThis is the default; the option can be used to reset the effect of \n--with_header/--header_only.\n" - , - "default":false - } - - - , - "count": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Instead of printing the alignments, only count them and print the total number", - "help_text": "Type: `boolean_true`, default: `false`. Instead of printing the alignments, only count them and print the total number.\nAll filter options, such as --require_flags, --excl_flags, and --min_MQ, are taken\ninto account. The --unmap option is ignored in this mode.\n" - , - "default":false - } - - - , - "output_unselected": { - "type": - "string", - "description": "Type: `file`. Write alignments that are not selected by the various filter options to FILE", - "help_text": "Type: `file`. Write alignments that are not selected by the various filter options to FILE.\nWhen this option is used, all alignments (or all alignments intersecting the regions\nspecified) are written to either the output file or this file, but never both.\n" - - } - - - , - "unmap": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Set the UNMAP flag on alignments that are not selected by the filter options", - "help_text": "Type: `boolean_true`, default: `false`. Set the UNMAP flag on alignments that are not selected by the filter options.\nThese alignments are then written to the normal output. This is not compatible\nwith --output_unselected.\n" - , - "default":false - } - - - , - "read_group": { - "type": - "string", - "description": "Type: `string`. Output alignments in read group STR [null]", - "help_text": "Type: `string`. Output alignments in read group STR [null]. Note that records with no RG tag will also be output\nwhen using this option. This behaviour may change in a future release.\n" - - } - - - , - "tag": { - "type": - "string", - "description": "Type: `string`. Only output alignments with tag STR1 and associated value STR2, which can be a string or an integer\n[null]", - "help_text": "Type: `string`. Only output alignments with tag STR1 and associated value STR2, which can be a string or an integer\n[null].\nThe value can be omitted, in which case only the tag is considered.\nNote that this option does not specify a tag type. For example, use --tag XX:42 to select alignments\nwith an XX:i:42 field, not --tag XX:i:42.\n" - - } - - - , - "tag_file": { - "type": - "string", - "description": "Type: `file`. Only output alignments with tag STR and associated values listed in FILE", - "help_text": "Type: `file`. Only output alignments with tag STR and associated values listed in FILE.\n" - - } - - - , - "min_MQ": { - "type": - "integer", - "description": "Type: `integer`, default: `0`. Skip alignments with MAPQ smaller than INT", - "help_text": "Type: `integer`, default: `0`. Skip alignments with MAPQ smaller than INT.\n" - , - "default":0 - } - - - , - "library": { - "type": - "string", - "description": "Type: `string`. Only output alignments in library STR", - "help_text": "Type: `string`. Only output alignments in library STR.\n" - - } - - - , - "min_qlen": { - "type": - "integer", - "description": "Type: `integer`, default: `0`. Only output alignments with number of CIGAR bases consuming query sequence \u003e= INT", - "help_text": "Type: `integer`, default: `0`. Only output alignments with number of CIGAR bases consuming query sequence \u003e= INT.\n" - , - "default":0 - } - - - , - "expr": { - "type": - "string", - "description": "Type: `string`. Only include alignments that match the filter expression STR", - "help_text": "Type: `string`. Only include alignments that match the filter expression STR. The syntax for these expressions is\ndescribed in the main samtools.\n" - - } - - - , - "require_flags": { - "type": - "string", - "description": "Type: `string`. Only output alignments with all bits set in FLAG present in the FLAG field", - "help_text": "Type: `string`. Only output alignments with all bits set in FLAG present in the FLAG field. FLAG can be specified\nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027 (i.e. /^0[0-7]+/),\nas a decimal number not beginning with \u00270\u0027 or as a comma-separated list of flag names.\n" - - } - - - , - "excl_flags": { - "type": - "string", - "description": "Type: `string`. Do not output alignments with any bits set in FLAG present in the FLAG field", - "help_text": "Type: `string`. Do not output alignments with any bits set in FLAG present in the FLAG field. FLAG can be specified\nin hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027 (i.e. /^0[0-7]+/),\nas a decimal number not beginning with \u00270\u0027 or as a comma-separated list of flag names.\n" - - } - - - , - "excl_all_flags": { - "type": - "integer", - "description": "Type: `integer`. Do not output alignments with all bits set in INT present in the FLAG field", - "help_text": "Type: `integer`. Do not output alignments with all bits set in INT present in the FLAG field. This is the opposite of\n--require_flags such that --require_flags 12 --exclude_all_flags 12 is the same as no filtering at all.\nFLAG can be specified in hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027\n(i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated list of flag names.\n" - - } - - - , - "incl_flags": { - "type": - "string", - "description": "Type: `string`. Only output alignments with any bit set in FLAG present in the FLAG field", - "help_text": "Type: `string`. Only output alignments with any bit set in FLAG present in the FLAG field. FLAG can be specified in hex\nby beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal by beginning with `0\u0027 (i.e. /^0[0-7]+/), as a decimal\nnumber not beginning with \u00270\u0027 or as a comma-separated list of flag names.\n" - - } - - - , - "remove_tag": { - "type": - "string", - "description": "Type: `string`. Read tag(s) to exclude from output (repeatable) [null]", - "help_text": "Type: `string`. Read tag(s) to exclude from output (repeatable) [null]. This can be a single tag or a comma separated list.\nAlternatively the option itself can be repeated multiple times.\nIf the list starts with a `^\u0027 then it is negated and treated as a request to remove all tags except those in STR.\nThe list may be empty, so --remove_tag ^ will remove all tags.\nNote that tags will only be removed from reads that pass filtering.\n" - - } - - - , - "keep_tag": { - "type": - "string", - "description": "Type: `string`. This keeps only tags listed in STR and is directly equivalent to --remove_tag ^STR", - "help_text": "Type: `string`. This keeps only tags listed in STR and is directly equivalent to --remove_tag ^STR. Specifying an empty list\nwill remove all tags. If both --keep_tag and --remove_tag are specified then --keep_tag has precedence.\nNote that tags will only be removed from reads that pass filtering.\n" - - } - - - , - "remove_B": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Collapse the backward CIGAR operation", - "help_text": "Type: `boolean_true`, default: `false`. Collapse the backward CIGAR operation.\n" - , - "default":false - } - - - , - "add_flags": { - "type": - "string", - "description": "Type: `string`. Adds flag(s) to read", - "help_text": "Type: `string`. Adds flag(s) to read. FLAG can be specified in hex by beginning with `0x\u0027 (i.e. /^0x[0-9A-F]+/), in octal\nby beginning with `0\u0027 (i.e. /^0[0-7]+/), as a decimal number not beginning with \u00270\u0027 or as a comma-separated\nlist of flag names.\n" - - } - - - , - "remove_flags": { - "type": - "string", - "description": "Type: `string`. Remove flag(s) from read", - "help_text": "Type: `string`. Remove flag(s) from read. FLAG is specified in the same way as with the --add_flags option.\n" - - } - - - , - "subsample": { - "type": - "number", - "description": "Type: `double`. Output only a proportion of the input alignments, as specified by 0", - "help_text": "Type: `double`. Output only a proportion of the input alignments, as specified by 0.0 \u003c= FLOAT \u003c= 1.0, which gives the fraction\nof templates/pairs to be kept. This subsampling acts in the same way on all of the alignment records in the same\ntemplate or read pair, so it never keeps a read but not its mate.\n" - - } - - - , - "subsample_seed": { - "type": - "integer", - "description": "Type: `integer`, default: `0`. Subsampling seed used to influence which subset of reads is kept", - "help_text": "Type: `integer`, default: `0`. Subsampling seed used to influence which subset of reads is kept. When subsampling data that has previously\nbeen subsampled, be sure to use a different seed value from those used previously; otherwise more reads will\nbe retained than expected.\n" - , - "default":0 - } - - - , - "fetch_pairs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Retrieve pairs even when the mate is outside of the requested region", - "help_text": "Type: `boolean_true`, default: `false`. Retrieve pairs even when the mate is outside of the requested region. Enabling this option also turns on the\nmulti-region iterator (-M). A region to search must be specified, either on the command-line, or using the\n--target_file option. The input file must be an indexed regular file.\nThis option first scans the requested region, using the RNEXT and PNEXT fields of the records that have the\nPAIRED flag set and pass other filtering options to find where paired reads are located. These locations are\nused to build an expanded region list, and a set of QNAMEs to allow from the new regions. It will then make\na second pass, collecting all reads from the originally-specified region list together with reads from additional\nlocations that match the allowed set of QNAMEs. Any other filtering options used will be applied to all reads\nfound during this second pass.\nAs this option links reads using RNEXT and PNEXT, it is important that these fields are set accurately. Use\n\u0027samtools fixmate\u0027 to correct them if necessary.\nNote that this option does not work with the --count, --output-unselected or --unmap options.\n" - , - "default":false - } - - - , - "customized_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Include customized index file as a part of arguments", - "help_text": "Type: `boolean_true`, default: `false`. Include customized index file as a part of arguments. See EXAMPLES section for sample of usage.\n" - , - "default":false - } - - - , - "sanitize": { - "type": - "string", - "description": "Type: `string`. Perform some sanity checks on the state of SAM record fields, fixing up common mistakes made by aligners", - "help_text": "Type: `string`. Perform some sanity checks on the state of SAM record fields, fixing up common mistakes made by aligners.\nThese include soft-clipping alignments when they extend beyond the end of the reference, marking records as\nunmapped when they have reference * or position 0, and ensuring unmapped alignments have no CIGAR or mapping\nquality for unmapped alignments and no MD, NM, CG or SM tags.\nFLAGs is a comma-separated list of keywords chosen from the following list.\n\nunmap: The UNMAPPED BAM flag. This is set for reads with position \u003c= 0, reference name \"*\" or reads starting\nbeyond the end of the reference. Note CIGAR \"*\" is permitted for mapped data so does not trigger this.\n\npos: Position and reference name fields. These may be cleared when a sequence is unmapped due to the\ncoordinates being beyond the end of the reference. Selecting this may change the sort order of the file,\nso it is not a part of the on compound argument.\nmqual: Mapping quality. This is set to zero for unmapped reads.\ncigar: Modifies CIGAR fields, either by adding soft-clips for reads that overlap the end of the reference or\n by clearing it for unmapped reads.\naux: For unmapped data, some auxiliary fields are meaningless and will be removed. These include NM, MD, CG and SM.\noff: Perform no sanity fixing. This is the default\non: Sanitize data in a way that guarantees the same sort order. This is everything except for pos.\nall: All sanitizing options, including pos.\n" - - } - - - , - "no_PG": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not add a @PG line to the header of the output file", - "help_text": "Type: `boolean_true`, default: `false`. Do not add a @PG line to the header of the output file.\n" - , - "default":false - } - - - , - "input_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single input file format option in the form of OPTION or OPTION=VALUE.\n" - - } - - - , - "output_fmt": { - "type": - "string", - "description": "Type: `string`. Specify output format (SAM, BAM, CRAM)", - "help_text": "Type: `string`. Specify output format (SAM, BAM, CRAM).\n" - - } - - - , - "output_fmt_option": { - "type": - "string", - "description": "Type: `string`. Specify a single output file format option in the form of OPTION or OPTION=VALUE", - "help_text": "Type: `string`. Specify a single output file format option in the form of OPTION or OPTION=VALUE.\n" - - } - - - , - "write_index": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Automatically index the output files", - "help_text": "Type: `boolean_true`, default: `false`. Automatically index the output files.\n" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "samtools_view", + "description": "Views and converts SAM/BAM/CRAM files.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input SAM, BAM, or CRAM file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "fai_reference": { + "type": "string", + "format": "path", + "description": "A tab-delimited FILE", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "reference": { + "type": "string", + "format": "path", + "description": "A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools faidx.\nIf an index is not present one will be generated for you, if the reference file is local.\nIf the reference file is not local, but is accessed instead via an https://, s3:// or other URL,\nthe index file will need to be supplied by the server alongside the reference", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "target_file": { + "type": "string", + "format": "path", + "description": "Only output alignments overlapping the input BED FILE [null].\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "region_file": { + "type": "string", + "format": "path", + "description": "Use an index and multi-region iterator to only output alignments overlapping the input BED FILE.\nEquivalent to --use_index --target_file FILE.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "qname_file": { + "type": "string", + "format": "path", + "description": "Output only alignments with read names listed in FILE", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "read_group_file": { + "type": "string", + "format": "path", + "description": "Output alignments in read groups listed in FILE [null]", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "use_index": { + "type": "boolean", + "description": "Use the multi-region iterator on the union of a BED file and command-line region arguments.\nThis avoids re-reading the same regions of files so can sometimes be much faster", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output to FILE instead of [stdout].", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"output.bam\"`. ", + "default": "$id.$key.output.bam" + }, + "bam": { + "type": "boolean", + "description": "Output in the BAM format.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "cram": { + "type": "boolean", + "description": "Output in the CRAM format (requires --reference).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fast": { + "type": "boolean", + "description": "Enable fast compression", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "uncompressed": { + "type": "boolean", + "description": "Output uncompressed data", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "with_header": { + "type": "boolean", + "description": "Include the header in the output.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "header_only": { + "type": "boolean", + "description": "Output the header only.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_header": { + "type": "boolean", + "description": "When producing SAM format, output alignment records but not headers.\nThis is the default; the option can be used to reset the effect of \n--with_header/--header_only.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "count": { + "type": "boolean", + "description": "Instead of printing the alignments, only count them and print the total number.\nAll filter options, such as --require_flags, --excl_flags, and --min_MQ, are taken\ninto account", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_unselected": { + "type": "string", + "format": "path", + "description": "Write alignments that are not selected by the various filter options to FILE.\nWhen this option is used, all alignments (or all alignments intersecting the regions\nspecified) are written to either the output file or this file, but never both.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "unmap": { + "type": "boolean", + "description": "Set the UNMAP flag on alignments that are not selected by the filter options.\nThese alignments are then written to the normal output", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "read_group": { + "type": "string", + "description": "Output alignments in read group STR [null]", + "help_text": "Type: `string`, multiple: `False`. " + }, + "tag": { + "type": "string", + "description": "Only output alignments with tag STR1 and associated value STR2, which can be a string or an integer\n[null].\nThe value can be omitted, in which case only the tag is considered.\nNote that this option does not specify a tag type", + "help_text": "Type: `string`, multiple: `False`. " + }, + "tag_file": { + "type": "string", + "format": "path", + "description": "Only output alignments with tag STR and associated values listed in FILE.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "min_MQ": { + "type": "integer", + "description": "Skip alignments with MAPQ smaller than INT.\n", + "help_text": "Type: `integer`, multiple: `False`, default: `0`. ", + "default": 0 + }, + "library": { + "type": "string", + "description": "Only output alignments in library STR.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "min_qlen": { + "type": "integer", + "description": "Only output alignments with number of CIGAR bases consuming query sequence >= INT.\n", + "help_text": "Type: `integer`, multiple: `False`, default: `0`. ", + "default": 0 + }, + "expr": { + "type": "string", + "description": "Only include alignments that match the filter expression STR", + "help_text": "Type: `string`, multiple: `False`. " + }, + "require_flags": { + "type": "string", + "description": "Only output alignments with all bits set in FLAG present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`. " + }, + "excl_flags": { + "type": "string", + "description": "Do not output alignments with any bits set in FLAG present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`. " + }, + "excl_all_flags": { + "type": "integer", + "description": "Do not output alignments with all bits set in INT present in the FLAG field", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "incl_flags": { + "type": "string", + "description": "Only output alignments with any bit set in FLAG present in the FLAG field", + "help_text": "Type: `string`, multiple: `False`. " + }, + "remove_tag": { + "type": "string", + "description": "Read tag(s) to exclude from output (repeatable) [null]", + "help_text": "Type: `string`, multiple: `False`. " + }, + "keep_tag": { + "type": "string", + "description": "This keeps only tags listed in STR and is directly equivalent to --remove_tag ^STR", + "help_text": "Type: `string`, multiple: `False`. " + }, + "remove_B": { + "type": "boolean", + "description": "Collapse the backward CIGAR operation.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "add_flags": { + "type": "string", + "description": "Adds flag(s) to read", + "help_text": "Type: `string`, multiple: `False`. " + }, + "remove_flags": { + "type": "string", + "description": "Remove flag(s) from read", + "help_text": "Type: `string`, multiple: `False`. " + }, + "subsample": { + "type": "number", + "description": "Output only a proportion of the input alignments, as specified by 0.0 <= FLOAT <= 1.0, which gives the fraction\nof templates/pairs to be kept", + "help_text": "Type: `double`, multiple: `False`. " + }, + "subsample_seed": { + "type": "integer", + "description": "Subsampling seed used to influence which subset of reads is kept", + "help_text": "Type: `integer`, multiple: `False`, default: `0`. ", + "default": 0 + }, + "fetch_pairs": { + "type": "boolean", + "description": "Retrieve pairs even when the mate is outside of the requested region", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "customized_index": { + "type": "boolean", + "description": "Include customized index file as a part of arguments", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sanitize": { + "type": "string", + "description": "Perform some sanity checks on the state of SAM record fields, fixing up common mistakes made by aligners.\nThese include soft-clipping alignments when they extend beyond the end of the reference, marking records as\nunmapped when they have reference * or position 0, and ensuring unmapped alignments have no CIGAR or mapping\nquality for unmapped alignments and no MD, NM, CG or SM tags.\nFLAGs is a comma-separated list of keywords chosen from the following list.\n\nunmap: The UNMAPPED BAM flag", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_PG": { + "type": "boolean", + "description": "Do not add a @PG line to the header of the output file.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input_fmt_option": { + "type": "string", + "description": "Specify a single input file format option in the form of OPTION or OPTION=VALUE.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "output_fmt": { + "type": "string", + "description": "Specify output format (SAM, BAM, CRAM).\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "output_fmt_option": { + "type": "string", + "description": "Specify a single output file format option in the form of OPTION or OPTION=VALUE.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "write_index": { + "type": "boolean", + "description": "Automatically index the output files.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index b046ffea..b8ea00f1 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -176,9 +176,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -203,6 +203,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index e04425d6..7b36fbf1 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3260,9 +3260,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3278,6 +3278,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json index 96e02772..4402ac6f 100644 --- a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json @@ -1,140 +1,85 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "seqtk_sample", -"description": "Subsamples sequences from FASTA/Q files.", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. The input FASTA/Q file", - "help_text": "Type: `file`, required. The input FASTA/Q file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. The output FASTA/Q file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. The output FASTA/Q file." - , - "default":"$id.$key.output" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "seed": { - "type": - "integer", - "description": "Type: `integer`, example: `42`. Seed for random generator", - "help_text": "Type: `integer`, example: `42`. Seed for random generator." - - } - - - , - "fraction_number": { - "type": - "number", - "description": "Type: `double`, required, example: `0.1`. Fraction or number of sequences to sample", - "help_text": "Type: `double`, required, example: `0.1`. Fraction or number of sequences to sample." - - } - - - , - "two_pass_mode": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Twice as slow but with much reduced memory", - "help_text": "Type: `boolean_true`, default: `false`. Twice as slow but with much reduced memory" - , - "default":false - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "seqtk_sample", + "description": "Subsamples sequences from FASTA/Q files.", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "The input FASTA/Q file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output FASTA/Q file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "seed": { + "type": "integer", + "description": "Seed for random generator.", + "help_text": "Type: `integer`, multiple: `False`, example: `42`. " + }, + "fraction_number": { + "type": "number", + "description": "Fraction or number of sequences to sample.", + "help_text": "Type: `double`, multiple: `False`, required, example: `0.1`. " + }, + "two_pass_mode": { + "type": "boolean", + "description": "Twice as slow but with much reduced memory", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index b2777da7..b3408655 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -11,10 +11,6 @@ authors: email: "theodorogtc@gmail.com" github: "tgaspe" linkedin: "theodoro-gasperin-terra-camargo" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -199,9 +195,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -226,6 +222,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index a9ecd50a..074d6dab 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3048,14 +3048,7 @@ meta = [ "email" : "theodorogtc@gmail.com", "github" : "tgaspe", "linkedin" : "theodoro-gasperin-terra-camargo" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3290,9 +3283,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3308,6 +3301,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json index 18b4a19b..07da8f8c 100644 --- a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json @@ -1,151 +1,93 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "seqtk_subseq", -"description": "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `input.fa`. The input FASTA/Q file", - "help_text": "Type: `file`, required, example: `input.fa`. The input FASTA/Q file." - - } - - - , - "name_list": { - "type": - "string", - "description": "Type: `file`, required, example: `list.lst`. List of sequence names (name", - "help_text": "Type: `file`, required, example: `list.lst`. List of sequence names (name.lst) or genomic regions (reg.bed) to extract.\n" - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `output.fa`. The output FASTA/Q file", - "help_text": "Type: `file`, required, default: `output.fa`. The output FASTA/Q file." - , - "default":"output.fa" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "tab": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. TAB delimited output", - "help_text": "Type: `boolean_true`, default: `false`. TAB delimited output." - , - "default":false - } - - - , - "strand_aware": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Strand aware", - "help_text": "Type: `boolean_true`, default: `false`. Strand aware." - , - "default":false - } - - - , - "sequence_line_length": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Sequence line length of input fasta file", - "help_text": "Type: `integer`, example: `0`. Sequence line length of input fasta file. Default: 0.\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "seqtk_subseq", + "description": "Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "The input FASTA/Q file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.fa\"`. " + }, + "name_list": { + "type": "string", + "format": "path", + "exists": true, + "description": "List of sequence names (name.lst) or genomic regions (reg.bed) to extract.\n", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"list.lst\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output FASTA/Q file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"output.fa\"`, direction: `output`. ", + "default": "output.fa" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "tab": { + "type": "boolean", + "description": "TAB delimited output.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "strand_aware": { + "type": "boolean", + "description": "Strand aware.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sequence_line_length": { + "type": "integer", + "description": "Sequence line length of input fasta file", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/sgdemux/.config.vsh.yaml b/target/nextflow/sgdemux/.config.vsh.yaml index 9d151d68..89ec61da 100644 --- a/target/nextflow/sgdemux/.config.vsh.yaml +++ b/target/nextflow/sgdemux/.config.vsh.yaml @@ -432,9 +432,9 @@ build_info: output: "target/nextflow/sgdemux" executable: "target/nextflow/sgdemux/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -459,6 +459,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/sgdemux/main.nf b/target/nextflow/sgdemux/main.nf index 577a9e5d..0b6456f9 100644 --- a/target/nextflow/sgdemux/main.nf +++ b/target/nextflow/sgdemux/main.nf @@ -3533,9 +3533,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sgdemux", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3551,6 +3551,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/sgdemux/nextflow_schema.json b/target/nextflow/sgdemux/nextflow_schema.json index 69413464..6d3ad3d0 100644 --- a/target/nextflow/sgdemux/nextflow_schema.json +++ b/target/nextflow/sgdemux/nextflow_schema.json @@ -1,340 +1,214 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "sgdemux", -"description": "Demultiplex sequence data generated on Singular Genomics\u0027 sequencing instruments.\n", -"type": "object", -"definitions": { - - - - "arguments" : { - "title": "Arguments", - "type": "object", - "description": "No description", - "properties": { - - - "read_structures": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. Read structures, one per input FASTQ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. Read structures, one per input FASTQ. Do not provide when using a path prefix for FASTQs" - - } - - - , - "allowed_mismatches": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Number of allowed mismatches between the observed barcode and the expected barcode", - "help_text": "Type: `integer`, example: `1`. Number of allowed mismatches between the observed barcode and the expected barcode" - - } - - - , - "min_delta": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. The minimum allowed difference between an observed barcode and the second closest expected barcode", - "help_text": "Type: `integer`, example: `2`. The minimum allowed difference between an observed barcode and the second closest expected barcode" - - } - - - , - "free_ns": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Number of N\u0027s to allow in a barcode without counting against the allowed_mismatches", - "help_text": "Type: `integer`, example: `1`. Number of N\u0027s to allow in a barcode without counting against the allowed_mismatches" - - } - - - , - "max_no_calls": { - "type": - "integer", - "description": "Type: `integer`. Max no-calls (N\u0027s) in a barcode before it is considered unmatchable", - "help_text": "Type: `integer`. Max no-calls (N\u0027s) in a barcode before it is considered unmatchable.\nA barcode with total N\u0027s greater than \u0027max_no_call\u0027 will be considered unmatchable.\n" - - } - - - , - "quality_mask_threshold": { - "type": - "string", - "description": "Type: List of `integer`, multiple_sep: `\";\"`. Mask template bases with quality scores less than specified value(s)", - "help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Mask template bases with quality scores less than specified value(s).\nSample barcode/index and UMI bases are never masked. If provided either a single value,\nor one value per FASTQ must be provided.\n" - - } - - - , - "filter_control_reads": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Filter out control reads", - "help_text": "Type: `boolean_true`, default: `false`. Filter out control reads" - , - "default":false - } - - - , - "filter_failing_quality": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Filter reads failing quality filter\n", - "help_text": "Type: `boolean_true`, default: `false`. Filter reads failing quality filter\n" - , - "default":false - } - - - , - "output_types": { - "type": - "string", - "description": "Type: List of `string`, example: `T`, multiple_sep: `\";\"`, choices: ``T`, `B`, `S`, `M``. The types of output FASTQs to write", - "help_text": "Type: List of `string`, example: `T`, multiple_sep: `\";\"`, choices: ``T`, `B`, `S`, `M``. The types of output FASTQs to write.\nFor each read structure, all segment types listed will be output to a FASTQ file.\n\nThese may be any of the following:\n - `T` - Template bases\n - `B` - Sample barcode bases\n - `M` - Molecular barcode bases\n - `S` - Skip bases\n" - - } - - - , - "undetermined_sample_name": { - "type": - "string", - "description": "Type: `string`, example: `Undetermined`. The sample name for undetermined reads (reads that do not match an expected barcode)\n", - "help_text": "Type: `string`, example: `Undetermined`. The sample name for undetermined reads (reads that do not match an expected barcode)\n" - - } - - - , - "most_unmatched_to_output": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. Output the most frequent \"unmatched\" barcodes up to this number", - "help_text": "Type: `integer`, example: `1000`. Output the most frequent \"unmatched\" barcodes up to this number.\nIf set to 0 unmatched barcodes will not be collected, improving overall performance.\n" - - } - - - , - "override_matcher": { - "type": - "string", - "description": "Type: `string`, choices: ``cached-hamming-distance`, `pre-compute``. If the sample barcodes are \u003e 12 bp long, a cached hamming distance matcher is used", - "help_text": "Type: `string`, choices: ``cached-hamming-distance`, `pre-compute``. If the sample barcodes are \u003e 12 bp long, a cached hamming distance matcher is used.\nIf the barcodes are less than or equal to 12 bp long, all possible matches are precomputed.\nThis option allows for overriding that heuristic.\n", - "enum": ["cached-hamming-distance", "pre-compute"] - - - } - - - , - "skip_read_name_check": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If this is true, then all the read names across FASTQs will not be enforced to be the same", - "help_text": "Type: `boolean_true`, default: `false`. If this is true, then all the read names across FASTQs will not be enforced to be the same.\nThis may be useful when the read names are known to be the same and performance matters.\nRegardless, the first read name in each FASTQ will always be checked.\n" - , - "default":false - } - - - , - "sample_barcode_in_fastq_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If this is true, then the sample barcode is expected to be in the FASTQ read header", - "help_text": "Type: `boolean_true`, default: `false`. If this is true, then the sample barcode is expected to be in the FASTQ read header.\nFor dual indexed data, the barcodes must be `+` (plus) delimited. Additionally, if true,\nthen neither index FASTQ files nor sample barcode segments in the read structure may be specified.\n" - , - "default":false - } - - - , - "metric_prefix": { - "type": - "string", - "description": "Type: `string`. Prepend this prefix to all output metric file names\n", - "help_text": "Type: `string`. Prepend this prefix to all output metric file names\n" - - } - - - , - "lane": { - "type": - "string", - "description": "Type: List of `integer`, multiple_sep: `\";\"`. Select a subset of lanes to demultiplex", - "help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Select a subset of lanes to demultiplex. Will cause only samples and input FASTQs with\nthe given `Lane`(s) to be demultiplexed. Samples without a lane will be ignored, and\nFASTQs without lane information will be ignored\n" - - } - - -} -}, - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "fastqs": { - "type": - "string", - "description": "Type: List of `file`, required, example: `sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq`, multiple_sep: `\";\"`. Path to the input FASTQs, or path prefix if not a file", - "help_text": "Type: List of `file`, required, example: `sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq`, multiple_sep: `\";\"`. Path to the input FASTQs, or path prefix if not a file" - - } - - - , - "sample_metadata": { - "type": - "string", - "description": "Type: `file`, required. Path to the sample metadata CSV file including sample names and barcode sequences", - "help_text": "Type: `file`, required. Path to the sample metadata CSV file including sample names and barcode sequences" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "sample_fastq": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files", - "help_text": "Type: `file`, required, default: `$id.$key.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files." - , - "default":"$id.$key.sample_fastq" - } - - - , - "metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.metrics.tsv`, example: `metrics.tsv`. Demultiplexing summary statisitcs:\n - control_reads_omitted: The number of reads that were omitted for being control reads", - "help_text": "Type: `file`, default: `$id.$key.metrics.tsv`, example: `metrics.tsv`. Demultiplexing summary statisitcs:\n - control_reads_omitted: The number of reads that were omitted for being control reads.\n - failing_reads_omitted: The number of reads that were omitted for having failed QC.\n - total_templates: The total number of template reads that were output.\n" - , - "default":"$id.$key.metrics.tsv" - } - - - , - "most_frequent_unmatched": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.most_frequent_unmatched.tsv`, example: `most_frequent_unmatched.tsv`. It contains the (approximate) counts of the most prevelant observed barcode sequences\nthat did not match to one of the expected barcodes", - "help_text": "Type: `file`, default: `$id.$key.most_frequent_unmatched.tsv`, example: `most_frequent_unmatched.tsv`. It contains the (approximate) counts of the most prevelant observed barcode sequences\nthat did not match to one of the expected barcodes. Can only be created when \u0027most_unmatched_to_output\u0027\nis not set to 0.\n" - , - "default":"$id.$key.most_frequent_unmatched.tsv" - } - - - , - "sample_barcode_hop_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.sample_barcode_hop_metrics.tsv`, example: `sample_barcode_hop_metrics.tsv`. File containing the frequently observed barcodes that are unexpected\ncombinations of expected barcodes in a dual-indexed run", - "help_text": "Type: `file`, default: `$id.$key.sample_barcode_hop_metrics.tsv`, example: `sample_barcode_hop_metrics.tsv`. File containing the frequently observed barcodes that are unexpected\ncombinations of expected barcodes in a dual-indexed run.\n" - , - "default":"$id.$key.sample_barcode_hop_metrics.tsv" - } - - - , - "per_project_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.per_project_metrics.tsv`, example: `per_project_metrics.tsv`. Aggregates the metrics by project (aggregates the metrics across samples with the same project) and\nhas the same columns as `--metrics`", - "help_text": "Type: `file`, default: `$id.$key.per_project_metrics.tsv`, example: `per_project_metrics.tsv`. Aggregates the metrics by project (aggregates the metrics across samples with the same project) and\nhas the same columns as `--metrics`. In this case, sample_ID will contain the project name (or None if no project is given).\nTHe barcode will contain all Ns. The undetermined sample will not be aggregated with any other sample.\n" - , - "default":"$id.$key.per_project_metrics.tsv" - } - - - , - "per_sample_metrics": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.per_sample_metrics.tsv`, example: `per_sample_metrics.tsv`. Tab-separated file containing statistics per sample", - "help_text": "Type: `file`, default: `$id.$key.per_sample_metrics.tsv`, example: `per_sample_metrics.tsv`. Tab-separated file containing statistics per sample.\n" - , - "default":"$id.$key.per_sample_metrics.tsv" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/arguments" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "sgdemux", + "description": "Demultiplex sequence data generated on Singular Genomics' sequencing instruments.\n", + "type": "object", + "$defs": { + "arguments": { + "title": "Arguments", + "type": "object", + "description": "No description", + "properties": { + "read_structures": { + "type": "array", + "items": { + "type": "string" + }, + "description": "Read structures, one per input FASTQ", + "help_text": "Type: `string`, multiple: `True`. " + }, + "allowed_mismatches": { + "type": "integer", + "description": "Number of allowed mismatches between the observed barcode and the expected barcode", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "min_delta": { + "type": "integer", + "description": "The minimum allowed difference between an observed barcode and the second closest expected barcode", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "free_ns": { + "type": "integer", + "description": "Number of N's to allow in a barcode without counting against the allowed_mismatches", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "max_no_calls": { + "type": "integer", + "description": "Max no-calls (N's) in a barcode before it is considered unmatchable.\nA barcode with total N's greater than 'max_no_call' will be considered unmatchable.\n", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "quality_mask_threshold": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Mask template bases with quality scores less than specified value(s).\nSample barcode/index and UMI bases are never masked", + "help_text": "Type: `integer`, multiple: `True`. " + }, + "filter_control_reads": { + "type": "boolean", + "description": "Filter out control reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "filter_failing_quality": { + "type": "boolean", + "description": "Filter reads failing quality filter\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_types": { + "type": "array", + "items": { + "type": "string" + }, + "description": "The types of output FASTQs to write.\nFor each read structure, all segment types listed will be output to a FASTQ file.\n\nThese may be any of the following:\n - `T` - Template bases\n - `B` - Sample barcode bases\n - `M` - Molecular barcode bases\n - `S` - Skip bases\n", + "help_text": "Type: `string`, multiple: `True`, example: `[\"T\"]`, choices: ``T`, `B`, `S`, `M``. " + }, + "undetermined_sample_name": { + "type": "string", + "description": "The sample name for undetermined reads (reads that do not match an expected barcode)\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"Undetermined\"`. " + }, + "most_unmatched_to_output": { + "type": "integer", + "description": "Output the most frequent \"unmatched\" barcodes up to this number.\nIf set to 0 unmatched barcodes will not be collected, improving overall performance.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "override_matcher": { + "type": "string", + "description": "If the sample barcodes are > 12 bp long, a cached hamming distance matcher is used.\nIf the barcodes are less than or equal to 12 bp long, all possible matches are precomputed.\nThis option allows for overriding that heuristic.\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``cached-hamming-distance`, `pre-compute``. ", + "enum": [ + "cached-hamming-distance", + "pre-compute" + ] + }, + "skip_read_name_check": { + "type": "boolean", + "description": "If this is true, then all the read names across FASTQs will not be enforced to be the same.\nThis may be useful when the read names are known to be the same and performance matters.\nRegardless, the first read name in each FASTQ will always be checked.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sample_barcode_in_fastq_header": { + "type": "boolean", + "description": "If this is true, then the sample barcode is expected to be in the FASTQ read header.\nFor dual indexed data, the barcodes must be `+` (plus) delimited", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "metric_prefix": { + "type": "string", + "description": "Prepend this prefix to all output metric file names\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "lane": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Select a subset of lanes to demultiplex", + "help_text": "Type: `integer`, multiple: `True`. " + } + } }, - - { - "$ref": "#/definitions/input" + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "fastqs": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Path to the input FASTQs, or path prefix if not a file", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq\"]`. " + }, + "sample_metadata": { + "type": "string", + "format": "path", + "exists": true, + "description": "Path to the sample metadata CSV file including sample names and barcode sequences", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "sample_fastq": { + "type": "string", + "format": "path", + "description": "The directory containing demultiplexed sample FASTQ files.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.sample_fastq\"`, direction: `output`, example: `\"output\"`. ", + "default": "$id.$key.sample_fastq" + }, + "metrics": { + "type": "string", + "format": "path", + "description": "Demultiplexing summary statisitcs:\n - control_reads_omitted: The number of reads that were omitted for being control reads.\n - failing_reads_omitted: The number of reads that were omitted for having failed QC.\n - total_templates: The total number of template reads that were output.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.metrics.tsv\"`, direction: `output`, example: `\"metrics.tsv\"`. ", + "default": "$id.$key.metrics.tsv" + }, + "most_frequent_unmatched": { + "type": "string", + "format": "path", + "description": "It contains the (approximate) counts of the most prevelant observed barcode sequences\nthat did not match to one of the expected barcodes", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.most_frequent_unmatched.tsv\"`, direction: `output`, example: `\"most_frequent_unmatched.tsv\"`. ", + "default": "$id.$key.most_frequent_unmatched.tsv" + }, + "sample_barcode_hop_metrics": { + "type": "string", + "format": "path", + "description": "File containing the frequently observed barcodes that are unexpected\ncombinations of expected barcodes in a dual-indexed run.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sample_barcode_hop_metrics.tsv\"`, direction: `output`, example: `\"sample_barcode_hop_metrics.tsv\"`. ", + "default": "$id.$key.sample_barcode_hop_metrics.tsv" + }, + "per_project_metrics": { + "type": "string", + "format": "path", + "description": "Aggregates the metrics by project (aggregates the metrics across samples with the same project) and\nhas the same columns as `--metrics`", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.per_project_metrics.tsv\"`, direction: `output`, example: `\"per_project_metrics.tsv\"`. ", + "default": "$id.$key.per_project_metrics.tsv" + }, + "per_sample_metrics": { + "type": "string", + "format": "path", + "description": "Tab-separated file containing statistics per sample.\n", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.per_sample_metrics.tsv\"`, direction: `output`, example: `\"per_sample_metrics.tsv\"`. ", + "default": "$id.$key.per_sample_metrics.tsv" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/arguments" + }, + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml index e2d138f1..c7527294 100644 --- a/target/nextflow/snpeff/.config.vsh.yaml +++ b/target/nextflow/snpeff/.config.vsh.yaml @@ -631,9 +631,9 @@ build_info: output: "target/nextflow/snpeff" executable: "target/nextflow/snpeff/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -658,6 +658,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf index f91de4f2..0d83bf1d 100644 --- a/target/nextflow/snpeff/main.nf +++ b/target/nextflow/snpeff/main.nf @@ -3785,9 +3785,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/snpeff", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3803,6 +3803,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/snpeff/nextflow_schema.json b/target/nextflow/snpeff/nextflow_schema.json index 1cbca5d1..cd654f4f 100644 --- a/target/nextflow/snpeff/nextflow_schema.json +++ b/target/nextflow/snpeff/nextflow_schema.json @@ -1,868 +1,493 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "snpeff", -"description": "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `test.vcf`. Input variants file", - "help_text": "Type: `file`, required, example: `test.vcf`. Input variants file." - - } - - - , - "genome_version": { - "type": - "string", - "description": "Type: `string`, required, example: `GRCh37.75`. Reference genome version", - "help_text": "Type: `string`, required, example: `GRCh37.75`. Reference genome version." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file", - "help_text": "Type: `file`, required, default: `$id.$key.output.vcf`, example: `out.vcf`. The output file." - , - "default":"$id.$key.output.vcf" - } - - - , - "summary": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.summary`, example: `summary_dir`. Summary file directory", - "help_text": "Type: `file`, default: `$id.$key.summary`, example: `summary_dir`. Summary file directory." - , - "default":"$id.$key.summary" - } - - - , - "genes": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.genes`, example: `genes_dir`. Txt file directory", - "help_text": "Type: `file`, default: `$id.$key.genes`, example: `genes_dir`. Txt file directory." - , - "default":"$id.$key.genes" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "chr": { - "type": - "string", - "description": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e", - "help_text": "Type: `string`. Prepend \u0027string\u0027 to chromosome name (e.g. \u0027chr1\u0027 instead of \u00271\u0027). Only on TXT output.\n" - - } - - - , - "classic": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs", - "help_text": "Type: `boolean_true`, default: `false`. Use old style annotations instead of Sequence Ontology and Hgvs." - , - "default":false - } - - - , - "csv_stats": { - "type": - "string", - "description": "Type: `file`. Create CSV summary file", - "help_text": "Type: `file`. Create CSV summary file." - - } - - - , - "download": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Download reference genome if not available", - "help_text": "Type: `boolean_true`, default: `false`. Download reference genome if not available." - , - "default":false - } - - - , - "input_format": { - "type": - "string", - "description": "Type: `string`. Input format [ vcf, bed ]", - "help_text": "Type: `string`. Input format [ vcf, bed ]. Default: VCF.\nexample: \"VCF\"\n" - - } - - - , - "file_list": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process", - "help_text": "Type: `boolean_true`, default: `false`. Input actually contains a list of files to process." - , - "default":false - } - - - , - "output_format": { - "type": - "string", - "description": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]", - "help_text": "Type: `string`, example: `VCF`. Output format [ vcf, gatk, bed, bedAnn ]. Default: VCF.\n" - - } - - - , - "stats": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Create HTML summary file", - "help_text": "Type: `boolean_true`, default: `false`. Create HTML summary file." - , - "default":false - } - - - , - "no_stats": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file", - "help_text": "Type: `boolean_true`, default: `false`. Do not create stats (summary) file." - , - "default":false - } - - -} -}, - - - "results filter options" : { - "title": "Results filter options", - "type": "object", - "description": "No description", - "properties": { - - - "fi": { - "type": - "string", - "description": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file", - "help_text": "Type: `file`. Only analyze changes that intersect with the intervals \nspecified in this file. This option can be used several times.\n" - - } - - - , - "no_downstream": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes", - "help_text": "Type: `boolean_true`, default: `false`. Do not show DOWNSTREAM changes" - , - "default":false - } - - - , - "no_intergenic": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes", - "help_text": "Type: `boolean_true`, default: `false`. Do not show INTERGENIC changes." - , - "default":false - } - - - , - "no_intron": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not show INTRON changes", - "help_text": "Type: `boolean_true`, default: `false`. Do not show INTRON changes." - , - "default":false - } - - - , - "no_upstream": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes", - "help_text": "Type: `boolean_true`, default: `false`. Do not show UPSTREAM changes." - , - "default":false - } - - - , - "no_utr": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes", - "help_text": "Type: `boolean_true`, default: `false`. Do not show 5_PRIME_UTR or 3_PRIME_UTR changes." - , - "default":false - } - - - , - "no": { - "type": - "string", - "description": "Type: `string`. Do not show \u0027EffectType\u0027", - "help_text": "Type: `string`. Do not show \u0027EffectType\u0027. This option can be used several times.\n" - - } - - -} -}, - - - "annotations options" : { - "title": "Annotations options", - "type": "object", - "description": "No description", - "properties": { - - - "cancer": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)", - "help_text": "Type: `boolean_true`, default: `false`. Perform \u0027cancer\u0027 comparisons (Somatic vs Germline)." - , - "default":false - } - - - , - "cancer_samples": { - "type": - "string", - "description": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples", - "help_text": "Type: `file`. Two column TXT file defining \u0027original \\t derived\u0027 samples." - - } - - - , - "fastaprot": { - "type": - "string", - "description": "Type: `file`. Create an output file containing the resulting protein sequences", - "help_text": "Type: `file`. Create an output file containing the resulting protein sequences.\n" - - } - - - , - "format_eff": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027)", - "help_text": "Type: `boolean_true`, default: `false`. Use \u0027EFF\u0027 field compatible with older versions (instead of \u0027ANN\u0027).\n" - , - "default":false - } - - - , - "gene_id": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)", - "help_text": "Type: `boolean_true`, default: `false`. Use gene ID instead of gene name (VCF output)." - , - "default":false - } - - - , - "hgvs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field", - "help_text": "Type: `boolean_true`, default: `false`. Use HGVS annotations for amino acid sub-field." - , - "default":false - } - - - , - "hgvs_old": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use old HGVS notation", - "help_text": "Type: `boolean_true`, default: `false`. Use old HGVS notation." - , - "default":false - } - - - , - "hgvs1_letter_aa": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation", - "help_text": "Type: `boolean_true`, default: `false`. Use one letter Amino acid codes in HGVS notation." - , - "default":false - } - - - , - "hgvs_tr_id": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation", - "help_text": "Type: `boolean_true`, default: `false`. Use transcript ID in HGVS notation." - , - "default":false - } - - - , - "lof": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags", - "help_text": "Type: `boolean_true`, default: `false`. Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n" - , - "default":false - } - - - , - "-no_hgvs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations", - "help_text": "Type: `boolean_true`, default: `false`. Do not add HGVS annotations." - , - "default":false - } - - - , - "no_lof": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations", - "help_text": "Type: `boolean_true`, default: `false`. Do not add LOF and NMD annotations." - , - "default":false - } - - - , - "no_shift_hgvs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end)", - "help_text": "Type: `boolean_true`, default: `false`. Do not shift variants according to HGVS notation (most 3prime end).\n" - , - "default":false - } - - - , - "oicr": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file", - "help_text": "Type: `boolean_true`, default: `false`. Add OICR tag in VCF file." - , - "default":false - } - - - , - "sequence_ontology": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms", - "help_text": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms." - , - "default":false - } - - -} -}, - - - "generic options" : { - "title": "Generic options", - "type": "object", - "description": "No description", - "properties": { - - - "config": { - "type": - "string", - "description": "Type: `file`. Specify config file", - "help_text": "Type: `file`. Specify config file" - - } - - - , - "config_option": { - "type": - "string", - "description": "Type: `string`. Override a config file option (name=value)", - "help_text": "Type: `string`. Override a config file option (name=value)." - - } - - - , - "debug": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)", - "help_text": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)." - , - "default":false - } - - - , - "data_dir": { - "type": - "string", - "description": "Type: `file`. Override data_dir parameter from config file", - "help_text": "Type: `file`. Override data_dir parameter from config file." - - } - - - , - "no_download": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally", - "help_text": "Type: `boolean_true`, default: `false`. Do not download a SnpEff database, if not available locally." - , - "default":false - } - - - , - "no_log": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server", - "help_text": "Type: `boolean_true`, default: `false`. Do not report usage statistics to server." - , - "default":false - } - - - , - "quiet": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)", - "help_text": "Type: `boolean_true`, default: `false`. Quiet mode (do not show any messages or errors)" - , - "default":false - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Verbose mode", - "help_text": "Type: `boolean_true`, default: `false`. Verbose mode." - , - "default":false - } - - -} -}, - - - "database options" : { - "title": "Database options", - "type": "object", - "description": "No description", - "properties": { - - - "canon": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only use canonical transcripts", - "help_text": "Type: `boolean_true`, default: `false`. Only use canonical transcripts." - , - "default":false - } - - - , - "canon_list": { - "type": - "string", - "description": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id \ntranscript_id\u0027 entries in \u003cfile\u003e", - "help_text": "Type: `file`. Only use canonical transcripts, replace some transcripts using the \u0027gene_id \ntranscript_id\u0027 entries in \u003cfile\u003e.\n" - - } - - - , - "tag": { - "type": - "string", - "description": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027", - "help_text": "Type: `string`. Only use transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n" - - } - - - , - "no_tag": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027", - "help_text": "Type: `boolean_true`, default: `false`. Filter out transcript having a tag \u0027tagName\u0027. This option can be used multiple times.\n" - , - "default":false - } - - - , - "interaction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)", - "help_text": "Type: `boolean_true`, default: `false`. Annotate using interactions (requires interaction database)." - , - "default":false - } - - - , - "interval": { - "type": - "string", - "description": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times)", - "help_text": "Type: `file`. Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).\n" - - } - - - , - "max_tsl": { - "type": - "integer", - "description": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e", - "help_text": "Type: `integer`. Only use transcripts having Transcript Support Level lower than \u003cTSL_number\u003e." - - } - - - , - "motif": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)", - "help_text": "Type: `boolean_true`, default: `false`. Annotate using motifs (requires Motif database)." - , - "default":false - } - - - , - "nextprot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)", - "help_text": "Type: `boolean_true`, default: `false`. Annotate using NextProt (requires NextProt database)." - , - "default":false - } - - - , - "no_genome": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e", - "help_text": "Type: `boolean_true`, default: `false`. Do not load any genomic database (e.g. annotate using custom files)." - , - "default":false - } - - - , - "no_expand_iub": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants", - "help_text": "Type: `boolean_true`, default: `false`. Disable IUB code expansion in input variants." - , - "default":false - } - - - , - "no_interaction": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable inteaction annotations", - "help_text": "Type: `boolean_true`, default: `false`. Disable inteaction annotations." - , - "default":false - } - - - , - "no_motif": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable motif annotations", - "help_text": "Type: `boolean_true`, default: `false`. Disable motif annotations." - , - "default":false - } - - - , - "no_nextprot": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Disable NextProt annotations", - "help_text": "Type: `boolean_true`, default: `false`. Disable NextProt annotations." - , - "default":false - } - - - , - "only_reg": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only use regulation tracks", - "help_text": "Type: `boolean_true`, default: `false`. Only use regulation tracks." - , - "default":false - } - - - , - "only_protein": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts", - "help_text": "Type: `boolean_true`, default: `false`. Only use protein coding transcripts." - , - "default":false - } - - - , - "only_tr": { - "type": - "string", - "description": "Type: `file`, example: `file.txt`. Only use the transcripts in this file", - "help_text": "Type: `file`, example: `file.txt`. Only use the transcripts in this file. Format: One transcript ID per line.\n" - - } - - - , - "reg": { - "type": - "string", - "description": "Type: `string`. Regulation track to use (this option can be used add several times)", - "help_text": "Type: `string`. Regulation track to use (this option can be used add several times)." - - } - - - , - "ss": { - "type": - "integer", - "description": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases", - "help_text": "Type: `integer`. Set size for splice sites (donor and acceptor) in bases. Default: 2.\n" - - } - - - , - "splice_region_exon_size": { - "type": - "integer", - "description": "Type: `integer`. Set size for splice site region within exons", - "help_text": "Type: `integer`. Set size for splice site region within exons. Default: 3 bases.\n" - - } - - - , - "splice_region_intron_min": { - "type": - "integer", - "description": "Type: `integer`. Set minimum number of bases for splice site region within intron", - "help_text": "Type: `integer`. Set minimum number of bases for splice site region within intron. Default: 3 bases.\n" - - } - - - , - "splice_region_intron_max": { - "type": - "integer", - "description": "Type: `integer`. Set maximum number of bases for splice site region within intron", - "help_text": "Type: `integer`. Set maximum number of bases for splice site region within intron. Default: 8 bases.\n" - - } - - - , - "strict": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i", - "help_text": "Type: `boolean_true`, default: `false`. Only use \u0027validated\u0027 transcripts (i.e. sequence has been checked)." - , - "default":false - } - - - , - "ud": { - "type": - "integer", - "description": "Type: `integer`. Set upstream downstream interval length (in bases)", - "help_text": "Type: `integer`. Set upstream downstream interval length (in bases)." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "snpeff", + "description": "Genetic variant annotation, and functional effect prediction toolbox. \nIt annotates and predicts the effects of genetic variants on genes and \nproteins (such as amino acid changes).\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input variants file.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"test.vcf\"`. " + }, + "genome_version": { + "type": "string", + "description": "Reference genome version.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"GRCh37.75\"`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "The output file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.vcf\"`, direction: `output`, example: `\"out.vcf\"`. ", + "default": "$id.$key.output.vcf" + }, + "summary": { + "type": "string", + "format": "path", + "description": "Summary file directory.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.summary\"`, direction: `output`, example: `\"summary_dir\"`. ", + "default": "$id.$key.summary" + }, + "genes": { + "type": "string", + "format": "path", + "description": "Txt file directory.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.genes\"`, direction: `output`, example: `\"genes_dir\"`. ", + "default": "$id.$key.genes" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "chr": { + "type": "string", + "description": "Prepend 'string' to chromosome name (e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "classic": { + "type": "boolean", + "description": "Use old style annotations instead of Sequence Ontology and Hgvs.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "csv_stats": { + "type": "string", + "format": "path", + "description": "Create CSV summary file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "download": { + "type": "boolean", + "description": "Download reference genome if not available.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input_format": { + "type": "string", + "description": "Input format [ vcf, bed ]", + "help_text": "Type: `string`, multiple: `False`. " + }, + "file_list": { + "type": "boolean", + "description": "Input actually contains a list of files to process.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_format": { + "type": "string", + "description": "Output format [ vcf, gatk, bed, bedAnn ]", + "help_text": "Type: `string`, multiple: `False`, example: `\"VCF\"`. " + }, + "stats": { + "type": "boolean", + "description": "Create HTML summary file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_stats": { + "type": "boolean", + "description": "Do not create stats (summary) file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/results filter options" + "results filter options": { + "title": "Results filter options", + "type": "object", + "description": "No description", + "properties": { + "fi": { + "type": "string", + "format": "path", + "description": "Only analyze changes that intersect with the intervals \nspecified in this file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "no_downstream": { + "type": "boolean", + "description": "Do not show DOWNSTREAM changes", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_intergenic": { + "type": "boolean", + "description": "Do not show INTERGENIC changes.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_intron": { + "type": "boolean", + "description": "Do not show INTRON changes.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_upstream": { + "type": "boolean", + "description": "Do not show UPSTREAM changes.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_utr": { + "type": "boolean", + "description": "Do not show 5_PRIME_UTR or 3_PRIME_UTR changes.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no": { + "type": "string", + "description": "Do not show 'EffectType'", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/annotations options" + "annotations options": { + "title": "Annotations options", + "type": "object", + "description": "No description", + "properties": { + "cancer": { + "type": "boolean", + "description": "Perform 'cancer' comparisons (Somatic vs Germline).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "cancer_samples": { + "type": "string", + "format": "path", + "description": "Two column TXT file defining 'original \\t derived' samples.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "fastaprot": { + "type": "string", + "format": "path", + "description": "Create an output file containing the resulting protein sequences.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "format_eff": { + "type": "boolean", + "description": "Use 'EFF' field compatible with older versions (instead of 'ANN').\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gene_id": { + "type": "boolean", + "description": "Use gene ID instead of gene name (VCF output).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hgvs": { + "type": "boolean", + "description": "Use HGVS annotations for amino acid sub-field.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hgvs_old": { + "type": "boolean", + "description": "Use old HGVS notation.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hgvs1_letter_aa": { + "type": "boolean", + "description": "Use one letter Amino acid codes in HGVS notation.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "hgvs_tr_id": { + "type": "boolean", + "description": "Use transcript ID in HGVS notation.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "lof": { + "type": "boolean", + "description": "Add loss of function (LOF) and Nonsense mediated decay (NMD) tags.\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "-no_hgvs": { + "type": "boolean", + "description": "Do not add HGVS annotations.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_lof": { + "type": "boolean", + "description": "Do not add LOF and NMD annotations.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_shift_hgvs": { + "type": "boolean", + "description": "Do not shift variants according to HGVS notation (most 3prime end).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "oicr": { + "type": "boolean", + "description": "Add OICR tag in VCF file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sequence_ontology": { + "type": "boolean", + "description": "Use Sequence Ontology terms.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/generic options" + "generic options": { + "title": "Generic options", + "type": "object", + "description": "No description", + "properties": { + "config": { + "type": "string", + "format": "path", + "description": "Specify config file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "config_option": { + "type": "string", + "description": "Override a config file option (name=value).", + "help_text": "Type: `string`, multiple: `False`. " + }, + "debug": { + "type": "boolean", + "description": "Debug mode (very verbose).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "data_dir": { + "type": "string", + "format": "path", + "description": "Override data_dir parameter from config file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "no_download": { + "type": "boolean", + "description": "Do not download a SnpEff database, if not available locally.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_log": { + "type": "boolean", + "description": "Do not report usage statistics to server.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "quiet": { + "type": "boolean", + "description": "Quiet mode (do not show any messages or errors)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "boolean", + "description": "Verbose mode.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/database options" + "database options": { + "title": "Database options", + "type": "object", + "description": "No description", + "properties": { + "canon": { + "type": "boolean", + "description": "Only use canonical transcripts.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "canon_list": { + "type": "string", + "format": "path", + "description": "Only use canonical transcripts, replace some transcripts using the 'gene_id \ntranscript_id' entries in .\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "tag": { + "type": "string", + "description": "Only use transcript having a tag 'tagName'", + "help_text": "Type: `string`, multiple: `False`. " + }, + "no_tag": { + "type": "boolean", + "description": "Filter out transcript having a tag 'tagName'", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "interaction": { + "type": "boolean", + "description": "Annotate using interactions (requires interaction database).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "interval": { + "type": "string", + "format": "path", + "description": "Use a custom intervals in TXT/BED/BigBed/VCF/GFF file (you may use this option many times).\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "max_tsl": { + "type": "integer", + "description": "Only use transcripts having Transcript Support Level lower than .", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "motif": { + "type": "boolean", + "description": "Annotate using motifs (requires Motif database).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "nextprot": { + "type": "boolean", + "description": "Annotate using NextProt (requires NextProt database).", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_genome": { + "type": "boolean", + "description": "Do not load any genomic database (e.g", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_expand_iub": { + "type": "boolean", + "description": "Disable IUB code expansion in input variants.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_interaction": { + "type": "boolean", + "description": "Disable inteaction annotations.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_motif": { + "type": "boolean", + "description": "Disable motif annotations.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_nextprot": { + "type": "boolean", + "description": "Disable NextProt annotations.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "only_reg": { + "type": "boolean", + "description": "Only use regulation tracks.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "only_protein": { + "type": "boolean", + "description": "Only use protein coding transcripts.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "only_tr": { + "type": "string", + "format": "path", + "description": "Only use the transcripts in this file", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"file.txt\"`. " + }, + "reg": { + "type": "string", + "description": "Regulation track to use (this option can be used add several times).", + "help_text": "Type: `string`, multiple: `False`. " + }, + "ss": { + "type": "integer", + "description": "Set size for splice sites (donor and acceptor) in bases", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "splice_region_exon_size": { + "type": "integer", + "description": "Set size for splice site region within exons", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "splice_region_intron_min": { + "type": "integer", + "description": "Set minimum number of bases for splice site region within intron", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "splice_region_intron_max": { + "type": "integer", + "description": "Set maximum number of bases for splice site region within intron", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "strict": { + "type": "boolean", + "description": "Only use 'validated' transcripts (i.e", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ud": { + "type": "integer", + "description": "Set upstream downstream interval length (in bases).", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/results filter options" + }, + { + "$ref": "#/$defs/annotations options" + }, + { + "$ref": "#/$defs/generic options" + }, + { + "$ref": "#/$defs/database options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 86587e8f..b9fb1869 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -597,9 +597,9 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -624,6 +624,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index be029ce4..5e4d48ea 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3690,9 +3690,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sortmerna", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3708,6 +3708,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/sortmerna/nextflow_schema.json b/target/nextflow/sortmerna/nextflow_schema.json index f3c2fcdc..1915b7b2 100644 --- a/target/nextflow/sortmerna/nextflow_schema.json +++ b/target/nextflow/sortmerna/nextflow_schema.json @@ -1,614 +1,373 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "sortmerna", -"description": "Local sequence alignment tool for filtering, mapping and clustering. The main \napplication of SortMeRNA is filtering rRNA from metatranscriptomic data.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Reads are paired-end", - "help_text": "Type: `boolean_true`, default: `false`. Reads are paired-end. If a single reads file is provided, use this option \nto indicate the file contains interleaved paired reads when neither\n\u0027paired_in\u0027 | \u0027paired_out\u0027 | \u0027out2\u0027 | \u0027sout\u0027 are specified.\n" - , - "default":false - } - - - , - "input": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Input fastq", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Input fastq" - - } - - - , - "ref": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. Reference fasta file(s) for rRNA database", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference fasta file(s) for rRNA database." - - } - - - , - "ribo_database_manifest": { - "type": - "string", - "description": "Type: `file`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA", - "help_text": "Type: `file`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.log.log`, example: `$id.sortmerna.log`. Sortmerna log file", - "help_text": "Type: `file`, default: `$id.$key.log.log`, example: `$id.sortmerna.log`. Sortmerna log file." - , - "default":"$id.$key.log.log" - } - - - , - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output", - "help_text": "Type: `file`, default: `$id.$key.output`. Directory and file prefix for aligned output. The appropriate extension: \n(fasta|fastq|blast|sam|etc) is automatically added.\nIf \u0027dir\u0027 is not specified, the output is created in the WORKDIR/out/.\nIf \u0027pfx\u0027 is not specified, the prefix \u0027aligned\u0027 is used.\n" - , - "default":"$id.$key.output" - } - - - , - "other": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix", - "help_text": "Type: `file`, default: `$id.$key.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx." - , - "default":"$id.$key.other" - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "kvdb": { - "type": - "string", - "description": "Type: `string`. Path to directory of the key-value database file, used for storing the alignment results", - "help_text": "Type: `string`. Path to directory of the key-value database file, used for storing the alignment results." - - } - - - , - "idx_dir": { - "type": - "string", - "description": "Type: `string`. Path to the directory for storing the reference index files", - "help_text": "Type: `string`. Path to the directory for storing the reference index files." - - } - - - , - "readb": { - "type": - "string", - "description": "Type: `string`. Path to the directory for storing pre-processed reads", - "help_text": "Type: `string`. Path to the directory for storing pre-processed reads." - - } - - - , - "fastx": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output aligned reads into FASTA/FASTQ file", - "help_text": "Type: `boolean_true`, default: `false`. Output aligned reads into FASTA/FASTQ file" - , - "default":false - } - - - , - "sam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output SAM alignment for aligned reads", - "help_text": "Type: `boolean_true`, default: `false`. Output SAM alignment for aligned reads." - , - "default":false - } - - - , - "sq": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add SQ tags to the SAM file", - "help_text": "Type: `boolean_true`, default: `false`. Add SQ tags to the SAM file" - , - "default":false - } - - - , - "blast": { - "type": - "string", - "description": "Type: `string`, choices: ``0`, `1`, `1 cigar`, `1 cigar qcov`, `1 cigar qcov qstrand``. Blast options:\n* \u00270\u0027 - pairwise\n* \u00271\u0027 - tabular(Blast - m 8 format)\n* \u00271 cigar\u0027 - tabular + column for CIGAR\n* \u00271 cigar qcov\u0027 - tabular + columns for CIGAR and query coverage\n* \u00271 cigar qcov qstrand\u0027 - tabular + columns for CIGAR, query coverage and strand\n", - "help_text": "Type: `string`, choices: ``0`, `1`, `1 cigar`, `1 cigar qcov`, `1 cigar qcov qstrand``. Blast options:\n* \u00270\u0027 - pairwise\n* \u00271\u0027 - tabular(Blast - m 8 format)\n* \u00271 cigar\u0027 - tabular + column for CIGAR\n* \u00271 cigar qcov\u0027 - tabular + columns for CIGAR and query coverage\n* \u00271 cigar qcov qstrand\u0027 - tabular + columns for CIGAR, query coverage and strand\n", - "enum": ["0", "1", "1 cigar", "1 cigar qcov", "1 cigar qcov qstrand"] - - - } - - - , - "num_alignments": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Report first INT alignments per read reaching E-value", - "help_text": "Type: `integer`, example: `0`. Report first INT alignments per read reaching E-value. If Int = 0, all alignments will be output. Default: \u00270\u0027\n" - - } - - - , - "min_lis": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. search all alignments having the first INT longest LIS", - "help_text": "Type: `integer`, example: `2`. search all alignments having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is\ncomputed using seeds\u0027 positions to expand hits into longer matches prior to Smith-Waterman alignment. Default: \u00272\u0027.\n" - - } - - - , - "print_all_reads": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. output null alignment strings for non-aligned reads to SAM and/or BLAST tabular files", - "help_text": "Type: `boolean_true`, default: `false`. output null alignment strings for non-aligned reads to SAM and/or BLAST tabular files." - , - "default":false - } - - - , - "paired_in": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In the case where a pair of reads is aligned with a score above the threshold, the output of the reads is controlled\nby the following options:\n* --paired_in and --paired_out are both false: Only one read per pair is output to the aligned fasta file", - "help_text": "Type: `boolean_true`, default: `false`. In the case where a pair of reads is aligned with a score above the threshold, the output of the reads is controlled\nby the following options:\n* --paired_in and --paired_out are both false: Only one read per pair is output to the aligned fasta file.\n* --paired_in is true and --paired_out is false: Both reads of the pair are output to the aligned fasta file.\n* --paired_in is false and --paired_out is true: Both reads are output the the other fasta file (if it is specified).\n" - , - "default":false - } - - - , - "paired_out": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. See description of --paired_in", - "help_text": "Type: `boolean_true`, default: `false`. See description of --paired_in." - , - "default":false - } - - - , - "out2": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output paired reads into separate files", - "help_text": "Type: `boolean_true`, default: `false`. Output paired reads into separate files. Must be used with \u0027--fastx\u0027. If a single reads file is provided, this options\nimplies interleaved paired reads. When used with \u0027sout\u0027, four (4) output files for aligned reads will be generated:\n\u0027aligned-paired-fwd, aligned-paired-rev, aligned-singleton-fwd, aligned-singleton-rev\u0027. If \u0027other\u0027 option is also used,\neight (8) output files will be generated.\n" - , - "default":false - } - - - , - "sout": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Separate paired and singleton aligned reads", - "help_text": "Type: `boolean_true`, default: `false`. Separate paired and singleton aligned reads. Must be used with \u0027--fastx\u0027. If a single reads file is provided,\nthis options implies interleaved paired reads. Cannot be used with \u0027--paired_in\u0027 or \u0027--paired_out\u0027.\n" - , - "default":false - } - - - , - "zip_out": { - "type": - "string", - "description": "Type: `string`, example: `-1`, choices: ``1`, `true`, `t`, `yes`, `y`, `0`, `false`, `f`, `no`, `n`, `-1``. Compress the output files", - "help_text": "Type: `string`, example: `-1`, choices: ``1`, `true`, `t`, `yes`, `y`, `0`, `false`, `f`, `no`, `n`, `-1``. Compress the output files. The possible values are: \n* \u00271/true/t/yes/y\u0027\n* \u00270/false/f/no/n\u0027\n*\u0027-1\u0027 (the same format as input - default)\nThe values are Not case sensitive.\n", - "enum": ["1", "true", "t", "yes", "y", "0", "false", "f", "no", "n", "-1"] - - - } - - - , - "match": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. Smith-Waterman score for a match (positive integer)", - "help_text": "Type: `integer`, example: `2`. Smith-Waterman score for a match (positive integer). Default: \u00272\u0027.\n" - - } - - - , - "mismatch": { - "type": - "integer", - "description": "Type: `integer`, example: `-3`. Smith-Waterman penalty for a mismatch (negative integer)", - "help_text": "Type: `integer`, example: `-3`. Smith-Waterman penalty for a mismatch (negative integer). Default: \u0027-3\u0027.\n" - - } - - - , - "gap_open": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. Smith-Waterman penalty for introducing a gap (positive integer)", - "help_text": "Type: `integer`, example: `5`. Smith-Waterman penalty for introducing a gap (positive integer). Default: \u00275\u0027.\n" - - } - - - , - "gap_ext": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. Smith-Waterman penalty for extending a gap (positive integer)", - "help_text": "Type: `integer`, example: `2`. Smith-Waterman penalty for extending a gap (positive integer). Default: \u00272\u0027.\n" - - } - - - , - "N": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. Smith-Waterman penalty for ambiguous letters (N\u0027s) scored as --mismatch", - "help_text": "Type: `integer`, example: `-1`. Smith-Waterman penalty for ambiguous letters (N\u0027s) scored as --mismatch. Default: \u0027-1\u0027.\n" - - } - - - , - "a": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Number of threads to use", - "help_text": "Type: `integer`, example: `1`. Number of threads to use. Default: \u00271\u0027.\n" - - } - - - , - "e": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. E-value threshold", - "help_text": "Type: `double`, example: `1.0`. E-value threshold. Default: \u00271\u0027.\n" - - } - - - , - "F": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Search only the forward strand", - "help_text": "Type: `boolean_true`, default: `false`. Search only the forward strand." - , - "default":false - } - - - , - "R": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Search only the reverse-complementary strand", - "help_text": "Type: `boolean_true`, default: `false`. Search only the reverse-complementary strand." - , - "default":false - } - - - , - "num_alignment": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. Report first INT alignments per read reaching E-value (--num_alignments 0 signifies all alignments will be output)", - "help_text": "Type: `integer`, example: `-1`. Report first INT alignments per read reaching E-value (--num_alignments 0 signifies all alignments will be output).\nDefault: \u0027-1\u0027\n" - - } - - - , - "best": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Report INT best alignments per read reaching E-value by searching --min_lis INT candidate alignments (--best 0\nsignifies all candidate alignments will be searched) Default: \u00271\u0027", - "help_text": "Type: `integer`, example: `1`. Report INT best alignments per read reaching E-value by searching --min_lis INT candidate alignments (--best 0\nsignifies all candidate alignments will be searched) Default: \u00271\u0027.\n" - - } - - - , - "verbose": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Verbose output", - "help_text": "Type: `boolean_true`, default: `false`. Verbose output." - , - "default":false - } - - -} -}, - - - "otu picking options" : { - "title": "OTU picking options", - "type": "object", - "description": "No description", - "properties": { - - - "id": { - "type": - "number", - "description": "Type: `double`, example: `0.97`. %id similarity threshold (the alignment must still pass the E-value threshold)", - "help_text": "Type: `double`, example: `0.97`. %id similarity threshold (the alignment must still pass the E-value threshold). Default: \u00270.97\u0027.\n" - - } - - - , - "coverage": { - "type": - "number", - "description": "Type: `double`, example: `0.97`. %query coverage threshold (the alignment must still pass the E-value threshold)", - "help_text": "Type: `double`, example: `0.97`. %query coverage threshold (the alignment must still pass the E-value threshold). Default: \u00270.97\u0027.\n" - - } - - - , - "de_novo": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. FASTA/FASTQ file for reads matching database \u003c %id off (set using --id) and \u003c %cov (set using --coverage)\n(alignment must still pass the E-value threshold)", - "help_text": "Type: `boolean_true`, default: `false`. FASTA/FASTQ file for reads matching database \u003c %id off (set using --id) and \u003c %cov (set using --coverage)\n(alignment must still pass the E-value threshold).\n" - , - "default":false - } - - - , - "otu_map": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output OTU map (input to QIIME\u0027s make_otu_table", - "help_text": "Type: `boolean_true`, default: `false`. Output OTU map (input to QIIME\u0027s make_otu_table.py).\n" - , - "default":false - } - - -} -}, - - - "advanced options" : { - "title": "Advanced options", - "type": "object", - "description": "No description", - "properties": { - - - "num_seed": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. Number of seeds matched before searching for candidate LIS", - "help_text": "Type: `integer`, example: `2`. Number of seeds matched before searching for candidate LIS. Default: \u00272\u0027.\n" - - } - - - , - "passes": { - "type": - "string", - "description": "Type: List of `integer`, multiple_sep: `\";\"`. Three intervals at which to place the seed on the read L,L/2,3 (L is the seed length set in ", - "help_text": "Type: List of `integer`, multiple_sep: `\";\"`. Three intervals at which to place the seed on the read L,L/2,3 (L is the seed length set in ./indexdb_rna).\n" - - } - - - , - "edge": { - "type": - "string", - "description": "Type: `string`, example: `4`. The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the\nreference sequence before performing Smith-Waterman alignment", - "help_text": "Type: `string`, example: `4`. The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the\nreference sequence before performing Smith-Waterman alignment. Default: \u00274\u0027.\n" - - } - - - , - "full_search": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Search for all 0-error and 1-error seed off matches in the index rather than stopping after finding a 0-error match\n(\u003c1% gain in sensitivity with up four-fold decrease in speed)", - "help_text": "Type: `boolean_true`, default: `false`. Search for all 0-error and 1-error seed off matches in the index rather than stopping after finding a 0-error match\n(\u003c1% gain in sensitivity with up four-fold decrease in speed).\n" - , - "default":false - } - - -} -}, - - - "indexing options" : { - "title": "Indexing Options", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "integer", - "description": "Type: `integer`, example: `2`, choices: ``0`, `1`, `2``. Create index files for the reference database", - "help_text": "Type: `integer`, example: `2`, choices: ``0`, `1`, `2``. Create index files for the reference database. By default when this option is not used, the program checks the\nreference index and builds it if not already existing.\nThis can be changed by using \u0027-index\u0027 as follows:\n* \u0027-index 0\u0027 - skip indexing. If the index does not exist, the program will terminate\n and warn to build the index prior performing the alignment\n* \u0027-index 1\u0027 - only perform the indexing and terminate\n* \u0027-index 2\u0027 - the default behaviour, the same as when not using this option at all\n", - "enum": [0, 1, 2] - - - } - - - , - "-L": { - "type": - "number", - "description": "Type: `double`, example: `18.0`. Indexing seed length", - "help_text": "Type: `double`, example: `18.0`. Indexing seed length. Default: \u002718\u0027\n" - - } - - - , - "interval": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Index every Nth L-mer in the reference database", - "help_text": "Type: `integer`, example: `1`. Index every Nth L-mer in the reference database. Default: \u00271\u0027\n" - - } - - - , - "max_pos": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. Maximum number of positions to store for each unique L-mer", - "help_text": "Type: `integer`, example: `1000`. Maximum number of positions to store for each unique L-mer. Set to 0 to store all positions. Default: \u00271000\u0027\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "sortmerna", + "description": "Local sequence alignment tool for filtering, mapping and clustering. The main \napplication of SortMeRNA is filtering rRNA from metatranscriptomic data.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "paired": { + "type": "boolean", + "description": "Reads are paired-end", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Input fastq", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "ref": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "Reference fasta file(s) for rRNA database.", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "ribo_database_manifest": { + "type": "string", + "format": "path", + "description": "Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "log": { + "type": "string", + "format": "path", + "description": "Sortmerna log file.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log.log\"`, direction: `output`, example: `\"$id.sortmerna.log\"`. ", + "default": "$id.$key.log.log" + }, + "output": { + "type": "string", + "format": "path", + "description": "Directory and file prefix for aligned output", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + }, + "other": { + "type": "string", + "format": "path", + "description": "Create Non-aligned reads output file with this path/prefix", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.other\"`, direction: `output`. ", + "default": "$id.$key.other" + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "kvdb": { + "type": "string", + "description": "Path to directory of the key-value database file, used for storing the alignment results.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "idx_dir": { + "type": "string", + "description": "Path to the directory for storing the reference index files.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "readb": { + "type": "string", + "description": "Path to the directory for storing pre-processed reads.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "fastx": { + "type": "boolean", + "description": "Output aligned reads into FASTA/FASTQ file", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sam": { + "type": "boolean", + "description": "Output SAM alignment for aligned reads.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sq": { + "type": "boolean", + "description": "Add SQ tags to the SAM file", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "blast": { + "type": "string", + "description": "Blast options:\n* '0' - pairwise\n* '1' - tabular(Blast - m 8 format)\n* '1 cigar' - tabular + column for CIGAR\n* '1 cigar qcov' - tabular + columns for CIGAR and query coverage\n* '1 cigar qcov qstrand' - tabular + columns for CIGAR, query coverage and strand\n", + "help_text": "Type: `string`, multiple: `False`, choices: ``0`, `1`, `1 cigar`, `1 cigar qcov`, `1 cigar qcov qstrand``. ", + "enum": [ + "0", + "1", + "1 cigar", + "1 cigar qcov", + "1 cigar qcov qstrand" + ] + }, + "num_alignments": { + "type": "integer", + "description": "Report first INT alignments per read reaching E-value", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "min_lis": { + "type": "integer", + "description": "search all alignments having the first INT longest LIS", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "print_all_reads": { + "type": "boolean", + "description": "output null alignment strings for non-aligned reads to SAM and/or BLAST tabular files.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "paired_in": { + "type": "boolean", + "description": "In the case where a pair of reads is aligned with a score above the threshold, the output of the reads is controlled\nby the following options:\n* --paired_in and --paired_out are both false: Only one read per pair is output to the aligned fasta file.\n* --paired_in is true and --paired_out is false: Both reads of the pair are output to the aligned fasta file.\n* --paired_in is false and --paired_out is true: Both reads are output the the other fasta file (if it is specified).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "paired_out": { + "type": "boolean", + "description": "See description of --paired_in.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "out2": { + "type": "boolean", + "description": "Output paired reads into separate files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "sout": { + "type": "boolean", + "description": "Separate paired and singleton aligned reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "zip_out": { + "type": "string", + "description": "Compress the output files", + "help_text": "Type: `string`, multiple: `False`, example: `\"-1\"`, choices: ``1`, `true`, `t`, `yes`, `y`, `0`, `false`, `f`, `no`, `n`, `-1``. ", + "enum": [ + "1", + "true", + "t", + "yes", + "y", + "0", + "false", + "f", + "no", + "n", + "-1" + ] + }, + "match": { + "type": "integer", + "description": "Smith-Waterman score for a match (positive integer)", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "mismatch": { + "type": "integer", + "description": "Smith-Waterman penalty for a mismatch (negative integer)", + "help_text": "Type: `integer`, multiple: `False`, example: `-3`. " + }, + "gap_open": { + "type": "integer", + "description": "Smith-Waterman penalty for introducing a gap (positive integer)", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "gap_ext": { + "type": "integer", + "description": "Smith-Waterman penalty for extending a gap (positive integer)", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "N": { + "type": "integer", + "description": "Smith-Waterman penalty for ambiguous letters (N's) scored as --mismatch", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "a": { + "type": "integer", + "description": "Number of threads to use", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "e": { + "type": "number", + "description": "E-value threshold", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + }, + "F": { + "type": "boolean", + "description": "Search only the forward strand.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "R": { + "type": "boolean", + "description": "Search only the reverse-complementary strand.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "num_alignment": { + "type": "integer", + "description": "Report first INT alignments per read reaching E-value (--num_alignments 0 signifies all alignments will be output).\nDefault: '-1'\n", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "best": { + "type": "integer", + "description": "Report INT best alignments per read reaching E-value by searching --min_lis INT candidate alignments (--best 0\nsignifies all candidate alignments will be searched) Default: '1'.\n", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "verbose": { + "type": "boolean", + "description": "Verbose output.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/otu picking options" + "otu picking options": { + "title": "OTU picking options", + "type": "object", + "description": "No description", + "properties": { + "id": { + "type": "number", + "description": "%id similarity threshold (the alignment must still pass the E-value threshold)", + "help_text": "Type: `double`, multiple: `False`, example: `0.97`. " + }, + "coverage": { + "type": "number", + "description": "%query coverage threshold (the alignment must still pass the E-value threshold)", + "help_text": "Type: `double`, multiple: `False`, example: `0.97`. " + }, + "de_novo": { + "type": "boolean", + "description": "FASTA/FASTQ file for reads matching database < %id off (set using --id) and < %cov (set using --coverage)\n(alignment must still pass the E-value threshold).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "otu_map": { + "type": "boolean", + "description": "Output OTU map (input to QIIME's make_otu_table.py).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/advanced options" + "advanced options": { + "title": "Advanced options", + "type": "object", + "description": "No description", + "properties": { + "num_seed": { + "type": "integer", + "description": "Number of seeds matched before searching for candidate LIS", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "passes": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "Three intervals at which to place the seed on the read L,L/2,3 (L is the seed length set in ./indexdb_rna).\n", + "help_text": "Type: `integer`, multiple: `True`. " + }, + "edge": { + "type": "string", + "description": "The number (or percentage if followed by %) of nucleotides to add to each edge of the alignment region on the\nreference sequence before performing Smith-Waterman alignment", + "help_text": "Type: `string`, multiple: `False`, example: `\"4\"`. " + }, + "full_search": { + "type": "boolean", + "description": "Search for all 0-error and 1-error seed off matches in the index rather than stopping after finding a 0-error match\n(<1% gain in sensitivity with up four-fold decrease in speed).\n", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/indexing options" + "indexing options": { + "title": "Indexing Options", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "integer", + "description": "Create index files for the reference database", + "help_text": "Type: `integer`, multiple: `False`, example: `2`, choices: ``0`, `1`, `2``. ", + "enum": [ + 0, + 1, + 2 + ] + }, + "-L": { + "type": "number", + "description": "Indexing seed length", + "help_text": "Type: `double`, multiple: `False`, example: `18.0`. " + }, + "interval": { + "type": "integer", + "description": "Index every Nth L-mer in the reference database", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "max_pos": { + "type": "integer", + "description": "Maximum number of positions to store for each unique L-mer", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/otu picking options" + }, + { + "$ref": "#/$defs/advanced options" + }, + { + "$ref": "#/$defs/indexing options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index dd9d35a3..04c75b48 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2666,9 +2666,9 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -2693,6 +2693,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index c5ac465b..17f28e1b 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -6173,9 +6173,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -6191,6 +6191,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/star/star_align_reads/nextflow_schema.json b/target/nextflow/star/star_align_reads/nextflow_schema.json index b839aa83..11b78de1 100644 --- a/target/nextflow/star/star_align_reads/nextflow_schema.json +++ b/target/nextflow/star/star_align_reads/nextflow_schema.json @@ -1,2314 +1,1395 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "star_align_reads", -"description": "Aligns reads to a reference genome using STAR.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, example: `mysample_S1_L001_R1_001.fastq.gz`, multiple_sep: `\";\"`. The single-end or paired-end R1 FastQ files to be processed", - "help_text": "Type: List of `file`, required, example: `mysample_S1_L001_R1_001.fastq.gz`, multiple_sep: `\";\"`. The single-end or paired-end R1 FastQ files to be processed." - - } - - - , - "input_r2": { - "type": - "string", - "description": "Type: List of `file`, example: `mysample_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. The paired-end R2 FastQ files to be processed", - "help_text": "Type: List of `file`, example: `mysample_S1_L001_R2_001.fastq.gz`, multiple_sep: `\";\"`. The paired-end R2 FastQ files to be processed. Only required if --input is a paired-end R1 file." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "aligned_reads": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.aligned_reads.bam`, example: `aligned_reads.bam`. The output file containing the aligned reads", - "help_text": "Type: `file`, required, default: `$id.$key.aligned_reads.bam`, example: `aligned_reads.bam`. The output file containing the aligned reads." - , - "default":"$id.$key.aligned_reads.bam" - } - - - , - "reads_per_gene": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.reads_per_gene.tsv`, example: `reads_per_gene.tsv`. The output file containing the number of reads per gene", - "help_text": "Type: `file`, default: `$id.$key.reads_per_gene.tsv`, example: `reads_per_gene.tsv`. The output file containing the number of reads per gene." - , - "default":"$id.$key.reads_per_gene.tsv" - } - - - , - "unmapped": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unmapped.fastq`, example: `unmapped.fastq`. The output file containing the unmapped reads", - "help_text": "Type: `file`, default: `$id.$key.unmapped.fastq`, example: `unmapped.fastq`. The output file containing the unmapped reads." - , - "default":"$id.$key.unmapped.fastq" - } - - - , - "unmapped_r2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unmapped_r2.fastq`, example: `unmapped_r2.fastq`. The output file containing the unmapped R2 reads", - "help_text": "Type: `file`, default: `$id.$key.unmapped_r2.fastq`, example: `unmapped_r2.fastq`. The output file containing the unmapped R2 reads." - , - "default":"$id.$key.unmapped_r2.fastq" - } - - - , - "chimeric_junctions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.chimeric_junctions.tsv`, example: `chimeric_junctions.tsv`. The output file containing the chimeric junctions", - "help_text": "Type: `file`, default: `$id.$key.chimeric_junctions.tsv`, example: `chimeric_junctions.tsv`. The output file containing the chimeric junctions." - , - "default":"$id.$key.chimeric_junctions.tsv" - } - - - , - "log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.log.txt`, example: `log.txt`. The output file containing the log of the alignment process", - "help_text": "Type: `file`, default: `$id.$key.log.txt`, example: `log.txt`. The output file containing the log of the alignment process." - , - "default":"$id.$key.log.txt" - } - - - , - "splice_junctions": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.splice_junctions.tsv`, example: `splice_junctions.tsv`. The output file containing the splice junctions", - "help_text": "Type: `file`, default: `$id.$key.splice_junctions.tsv`, example: `splice_junctions.tsv`. The output file containing the splice junctions." - , - "default":"$id.$key.splice_junctions.tsv" - } - - - , - "reads_aligned_to_transcriptome": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.reads_aligned_to_transcriptome.bam`, example: `transcriptome_aligned.bam`. The output file containing the alignments to transcriptome in BAM formats", - "help_text": "Type: `file`, default: `$id.$key.reads_aligned_to_transcriptome.bam`, example: `transcriptome_aligned.bam`. The output file containing the alignments to transcriptome in BAM formats. This file is generated when --quantMode is set to TranscriptomeSAM." - , - "default":"$id.$key.reads_aligned_to_transcriptome.bam" - } - - -} -}, - - - "run parameters" : { - "title": "Run Parameters", - "type": "object", - "description": "No description", - "properties": { - - - "run_rng_seed": { - "type": - "integer", - "description": "Type: `integer`, example: `777`. random number generator seed", - "help_text": "Type: `integer`, example: `777`. random number generator seed." - - } - - -} -}, - - - "genome parameters" : { - "title": "Genome Parameters", - "type": "object", - "description": "No description", - "properties": { - - - "genome_dir": { - "type": - "string", - "description": "Type: `file`, required, example: `./GenomeDir`. path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)", - "help_text": "Type: `file`, required, example: `./GenomeDir`. path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)" - - } - - - , - "genome_load": { - "type": - "string", - "description": "Type: `string`, example: `NoSharedMemory`. mode of shared memory usage for the genome files", - "help_text": "Type: `string`, example: `NoSharedMemory`. mode of shared memory usage for the genome files. Only used with --runMode alignReads.\n\n- LoadAndKeep ... load genome into shared and keep it in memory after run\n- LoadAndRemove ... load genome into shared but remove it after run\n- LoadAndExit ... load genome into shared memory and exit, keeping the genome in memory for future runs\n- Remove ... do not map anything, just remove loaded genome from memory\n- NoSharedMemory ... do not use shared memory, each job will have its own private copy of the genome" - - } - - - , - "genome_fasta_files": { - "type": - "string", - "description": "Type: List of `file`, multiple_sep: `\";\"`. path(s) to the fasta files with the genome sequences, separated by spaces", - "help_text": "Type: List of `file`, multiple_sep: `\";\"`. path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped.\n\nRequired for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins)." - - } - - - , - "genome_file_sizes": { - "type": - "string", - "description": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. genome files exact sizes in bytes", - "help_text": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. genome files exact sizes in bytes. Typically, this should not be defined by the user." - - } - - - , - "genome_transform_output": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. which output to transform back to original genome\n\n- SAM ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. which output to transform back to original genome\n\n- SAM ... SAM/BAM alignments\n- SJ ... splice junctions (SJ.out.tab)\n- Quant ... quantifications (from --quant_mode option)\n- None ... no transformation of the output" - - } - - - , - "genome_chr_set_mitochondrial": { - "type": - "string", - "description": "Type: List of `string`, example: `chrM;M;MT`, multiple_sep: `\";\"`. names of the mitochondrial chromosomes", - "help_text": "Type: List of `string`, example: `chrM;M;MT`, multiple_sep: `\";\"`. names of the mitochondrial chromosomes. Presently only used for STARsolo statistics output/" - - } - - -} -}, - - - "splice junctions database" : { - "title": "Splice Junctions Database", - "type": "object", - "description": "No description", - "properties": { - - - "sjdb_file_chr_start_end": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. path to the files with genomic coordinates (chr \u003ctab\u003e start \u003ctab\u003e end \u003ctab\u003e strand) for the splice junction introns", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. path to the files with genomic coordinates (chr \u003ctab\u003e start \u003ctab\u003e end \u003ctab\u003e strand) for the splice junction introns. Multiple files can be supplied and will be concatenated." - - } - - - , - "sjdb_gtf_file": { - "type": - "string", - "description": "Type: `file`. path to the GTF file with annotations", - "help_text": "Type: `file`. path to the GTF file with annotations" - - } - - - , - "sjdb_gtf_chr_prefix": { - "type": - "string", - "description": "Type: `string`. prefix for chromosome names in a GTF file (e", - "help_text": "Type: `string`. prefix for chromosome names in a GTF file (e.g. \u0027chr\u0027 for using ENSMEBL annotations with UCSC genomes)" - - } - - - , - "sjdb_gtf_feature_exon": { - "type": - "string", - "description": "Type: `string`, example: `exon`. feature type in GTF file to be used as exons for building transcripts", - "help_text": "Type: `string`, example: `exon`. feature type in GTF file to be used as exons for building transcripts" - - } - - - , - "sjdb_gtf_tag_exon_parent_transcript": { - "type": - "string", - "description": "Type: `string`, example: `transcript_id`. GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)", - "help_text": "Type: `string`, example: `transcript_id`. GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene": { - "type": - "string", - "description": "Type: `string`, example: `gene_id`. GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)", - "help_text": "Type: `string`, example: `gene_id`. GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene_name": { - "type": - "string", - "description": "Type: List of `string`, example: `gene_name`, multiple_sep: `\";\"`. GTF attribute name for parent gene name", - "help_text": "Type: List of `string`, example: `gene_name`, multiple_sep: `\";\"`. GTF attribute name for parent gene name" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene_type": { - "type": - "string", - "description": "Type: List of `string`, example: `gene_type;gene_biotype`, multiple_sep: `\";\"`. GTF attribute name for parent gene type", - "help_text": "Type: List of `string`, example: `gene_type;gene_biotype`, multiple_sep: `\";\"`. GTF attribute name for parent gene type" - - } - - - , - "sjdb_overhang": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)", - "help_text": "Type: `integer`, example: `100`. length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)" - - } - - - , - "sjdb_score": { - "type": - "integer", - "description": "Type: `integer`, example: `2`. extra alignment score for alignments that cross database junctions", - "help_text": "Type: `integer`, example: `2`. extra alignment score for alignments that cross database junctions" - - } - - - , - "sjdb_insert_save": { - "type": - "string", - "description": "Type: `string`, example: `Basic`. which files to save when sjdb junctions are inserted on the fly at the mapping step\n\n- Basic ", - "help_text": "Type: `string`, example: `Basic`. which files to save when sjdb junctions are inserted on the fly at the mapping step\n\n- Basic ... only small junction / transcript files\n- All ... all files including big Genome, SA and SAindex - this will create a complete genome directory" - - } - - -} -}, - - - "variation parameters" : { - "title": "Variation parameters", - "type": "object", - "description": "No description", - "properties": { - - - "var_vcf_file": { - "type": - "string", - "description": "Type: `string`. path to the VCF file that contains variation data", - "help_text": "Type: `string`. path to the VCF file that contains variation data. The 10th column should contain the genotype information, e.g. 0/1" - - } - - -} -}, - - - "read parameters" : { - "title": "Read Parameters", - "type": "object", - "description": "No description", - "properties": { - - - "read_files_type": { - "type": - "string", - "description": "Type: `string`, example: `Fastx`. format of input read files\n\n- Fastx ", - "help_text": "Type: `string`, example: `Fastx`. format of input read files\n\n- Fastx ... FASTA or FASTQ\n- SAM SE ... SAM or BAM single-end reads; for BAM use --read_files_command samtools view\n- SAM PE ... SAM or BAM paired-end reads; for BAM use --read_files_command samtools view" - - } - - - , - "read_files_sam_attr_keep": { - "type": - "string", - "description": "Type: List of `string`, example: `All`, multiple_sep: `\";\"`. for --read_files_type SAM SE/PE, which SAM tags to keep in the output BAM, e", - "help_text": "Type: List of `string`, example: `All`, multiple_sep: `\";\"`. for --read_files_type SAM SE/PE, which SAM tags to keep in the output BAM, e.g.: --readFilesSAMtagsKeep RG PL\n\n- All ... keep all tags\n- None ... do not keep any tags" - - } - - - , - "read_files_manifest": { - "type": - "string", - "description": "Type: `file`. path to the \"manifest\" file with the names of read files", - "help_text": "Type: `file`. path to the \"manifest\" file with the names of read files. The manifest file should contain 3 tab-separated columns:\n\npaired-end reads: read1_file_name $tab$ read2_file_name $tab$ read_group_line.\nsingle-end reads: read1_file_name $tab$ - $tab$ read_group_line.\nSpaces, but not tabs are allowed in file names.\nIf read_group_line does not start with ID:, it can only contain one ID field, and ID: will be added to it.\nIf read_group_line starts with ID:, it can contain several fields separated by $tab$, and all fields will be be copied verbatim into SAM @RG header line." - - } - - - , - "read_files_prefix": { - "type": - "string", - "description": "Type: `string`. prefix for the read files names, i", - "help_text": "Type: `string`. prefix for the read files names, i.e. it will be added in front of the strings in --readFilesIn" - - } - - - , - "read_files_command": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. command line to execute for each of the input file", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout\n\nFor example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc." - - } - - - , - "read_map_number": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. number of reads to map from the beginning of the file\n\n-1: map all reads", - "help_text": "Type: `integer`, example: `-1`. number of reads to map from the beginning of the file\n\n-1: map all reads" - - } - - - , - "read_mates_lengths_in": { - "type": - "string", - "description": "Type: `string`, example: `NotEqual`. Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same", - "help_text": "Type: `string`, example: `NotEqual`. Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations." - - } - - - , - "read_name_separator": { - "type": - "string", - "description": "Type: List of `string`, example: `/`, multiple_sep: `\";\"`. character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)", - "help_text": "Type: List of `string`, example: `/`, multiple_sep: `\";\"`. character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)" - - } - - - , - "read_quality_score_base": { - "type": - "integer", - "description": "Type: `integer`, example: `33`. number to be subtracted from the ASCII code to get Phred quality score", - "help_text": "Type: `integer`, example: `33`. number to be subtracted from the ASCII code to get Phred quality score" - - } - - -} -}, - - - "read clipping" : { - "title": "Read Clipping", - "type": "object", - "description": "No description", - "properties": { - - - "clip_adapter_type": { - "type": - "string", - "description": "Type: `string`, example: `Hamming`. adapter clipping type\n\n- Hamming ", - "help_text": "Type: `string`, example: `Hamming`. adapter clipping type\n\n- Hamming ... adapter clipping based on Hamming distance, with the number of mismatches controlled by --clip5pAdapterMMp\n- CellRanger4 ... 5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin Sosic: https://github.com/Martinsos/opal\n- None ... no adapter clipping, all other clip* parameters are disregarded" - - } - - - , - "clip3p_nbases": { - "type": - "string", - "description": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number(s) of bases to clip from 3p of each mate", - "help_text": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number(s) of bases to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates." - - } - - - , - "clip3p_adapter_seq": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. adapter sequences to clip from 3p of each mate", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. adapter sequences to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates.\n\n- polyA ... polyA sequence with the length equal to read length" - - } - - - , - "clip3p_adapter_mm_p": { - "type": - "string", - "description": "Type: List of `double`, example: `0.1`, multiple_sep: `\";\"`. max proportion of mismatches for 3p adapter clipping for each mate", - "help_text": "Type: List of `double`, example: `0.1`, multiple_sep: `\";\"`. max proportion of mismatches for 3p adapter clipping for each mate. If one value is given, it will be assumed the same for both mates." - - } - - - , - "clip3p_after_adapter_nbases": { - "type": - "string", - "description": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number of bases to clip from 3p of each mate after the adapter clipping", - "help_text": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number of bases to clip from 3p of each mate after the adapter clipping. If one value is given, it will be assumed the same for both mates." - - } - - - , - "clip5p_nbases": { - "type": - "string", - "description": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number(s) of bases to clip from 5p of each mate", - "help_text": "Type: List of `integer`, example: `0`, multiple_sep: `\";\"`. number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates." - - } - - -} -}, - - - "limits" : { - "title": "Limits", - "type": "object", - "description": "No description", - "properties": { - - - "limit_genome_generate_ram": { - "type": - "string", - "description": "Type: `long`, example: `31000000000`. maximum available RAM (bytes) for genome generation", - "help_text": "Type: `long`, example: `31000000000`. maximum available RAM (bytes) for genome generation" - - } - - - , - "limit_io_buffer_size": { - "type": - "string", - "description": "Type: List of `long`, example: `30000000;50000000`, multiple_sep: `\";\"`. max available buffers size (bytes) for input/output, per thread", - "help_text": "Type: List of `long`, example: `30000000;50000000`, multiple_sep: `\";\"`. max available buffers size (bytes) for input/output, per thread" - - } - - - , - "limit_out_sam_one_read_bytes": { - "type": - "string", - "description": "Type: `long`, example: `100000`. max size of the SAM record (bytes) for one read", - "help_text": "Type: `long`, example: `100000`. max size of the SAM record (bytes) for one read. Recommended value: \u003e(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax" - - } - - - , - "limit_out_sj_one_read": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. max number of junctions for one read (including all multi-mappers)", - "help_text": "Type: `integer`, example: `1000`. max number of junctions for one read (including all multi-mappers)" - - } - - - , - "limit_out_sj_collapsed": { - "type": - "integer", - "description": "Type: `integer`, example: `1000000`. max number of collapsed junctions", - "help_text": "Type: `integer`, example: `1000000`. max number of collapsed junctions" - - } - - - , - "limit_bam_sort_ram": { - "type": - "string", - "description": "Type: `long`, example: `0`. maximum available RAM (bytes) for sorting BAM", - "help_text": "Type: `long`, example: `0`. maximum available RAM (bytes) for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genome_load NoSharedMemory option." - - } - - - , - "limit_sjdb_insert_nsj": { - "type": - "integer", - "description": "Type: `integer`, example: `1000000`. maximum number of junctions to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run", - "help_text": "Type: `integer`, example: `1000000`. maximum number of junctions to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run" - - } - - - , - "limit_nreads_soft": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. soft limit on the number of reads", - "help_text": "Type: `integer`, example: `-1`. soft limit on the number of reads" - - } - - -} -}, - - - "output: general" : { - "title": "Output: general", - "type": "object", - "description": "No description", - "properties": { - - - "out_tmp_keep": { - "type": - "string", - "description": "Type: `string`. whether to keep the temporary files after STAR runs is finished\n\n- None ", - "help_text": "Type: `string`. whether to keep the temporary files after STAR runs is finished\n\n- None ... remove all temporary files\n- All ... keep all files" - - } - - - , - "out_std": { - "type": - "string", - "description": "Type: `string`, example: `Log`. which output will be directed to stdout (standard out)\n\n- Log ", - "help_text": "Type: `string`, example: `Log`. which output will be directed to stdout (standard out)\n\n- Log ... log messages\n- SAM ... alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out\n- BAM_Unsorted ... alignments in BAM format, unsorted. Requires --out_sam_type BAM Unsorted\n- BAM_SortedByCoordinate ... alignments in BAM format, sorted by coordinate. Requires --out_sam_type BAM SortedByCoordinate\n- BAM_Quant ... alignments to transcriptome in BAM format, unsorted. Requires --quant_mode TranscriptomeSAM" - - } - - - , - "out_reads_unmapped": { - "type": - "string", - "description": "Type: `string`. output of unmapped and partially mapped (i", - "help_text": "Type: `string`. output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).\n\n- None ... no output\n- Fastx ... output in separate fasta/fastq files, Unmapped.out.mate1/2" - - } - - - , - "out_qs_conversion_add": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. add this number to the quality score (e", - "help_text": "Type: `integer`, example: `0`. add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)" - - } - - - , - "out_multimapper_order": { - "type": - "string", - "description": "Type: `string`, example: `Old_2.4`. order of multimapping alignments in the output files\n\n- Old_2", - "help_text": "Type: `string`, example: `Old_2.4`. order of multimapping alignments in the output files\n\n- Old_2.4 ... quasi-random order used before 2.5.0\n- Random ... random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases." - - } - - -} -}, - - - "output: sam and bam" : { - "title": "Output: SAM and BAM", - "type": "object", - "description": "No description", - "properties": { - - - "out_sam_type": { - "type": - "string", - "description": "Type: List of `string`, example: `SAM`, multiple_sep: `\";\"`. type of SAM/BAM output\n\n1st word:\n- BAM ", - "help_text": "Type: List of `string`, example: `SAM`, multiple_sep: `\";\"`. type of SAM/BAM output\n\n1st word:\n- BAM ... output BAM without sorting\n- SAM ... output SAM without sorting\n- None ... no SAM/BAM output\n2nd, 3rd:\n- Unsorted ... standard unsorted\n- SortedByCoordinate ... sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limit_bam_sort_ram." - - } - - - , - "out_sam_mode": { - "type": - "string", - "description": "Type: `string`, example: `Full`. mode of SAM output\n\n- None ", - "help_text": "Type: `string`, example: `Full`. mode of SAM output\n\n- None ... no SAM output\n- Full ... full SAM output\n- NoQS ... full SAM but without quality scores" - - } - - - , - "out_sam_strand_field": { - "type": - "string", - "description": "Type: `string`. Cufflinks-like strand field flag\n\n- None ", - "help_text": "Type: `string`. Cufflinks-like strand field flag\n\n- None ... not used\n- intronMotif ... strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out." - - } - - - , - "out_sam_attributes": { - "type": - "string", - "description": "Type: List of `string`, example: `Standard`, multiple_sep: `\";\"`. a string of desired SAM attributes, in the order desired for the output SAM", - "help_text": "Type: List of `string`, example: `Standard`, multiple_sep: `\";\"`. a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.\n\n***Presets:\n- None ... no attributes\n- Standard ... NH HI AS nM\n- All ... NH HI AS nM NM MD jM jI MC ch\n***Alignment:\n- NH ... number of loci the reads maps to: =1 for unique mappers, \u003e1 for multimappers. Standard SAM tag.\n- HI ... multiple alignment index, starts with --out_sam_attr_ih_start (=1 by default). Standard SAM tag.\n- AS ... local alignment score, +1/-1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Stadnard SAM tag.\n- nM ... number of mismatches. For PE reads, sum over two mates.\n- NM ... edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.\n- MD ... string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.\n- jM ... intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.\n- jI ... start and end of introns for all junctions (1-based).\n- XS ... alignment strand according to --out_sam_strand_field.\n- MC ... mate\u0027s CIGAR string. Standard SAM tag.\n- ch ... marks all segment of all chimeric alingments for --chim_out_type WithinBAM output.\n- cN ... number of bases clipped from the read ends: 5\u0027 and 3\u0027\n***Variation:\n- vA ... variant allele\n- vG ... genomic coordinate of the variant overlapped by the read.\n- vW ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --wasp_output_mode SAMtag.\n- ha ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid .\n***STARsolo:\n- CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.\n- GX GN ... gene ID and gene name for unique-gene reads.\n- gx gn ... gene IDs and gene names for unique- and multi-gene reads.\n- CB UB ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --out_sam_type BAM SortedByCoordinate.\n- sM ... assessment of CB and UMI.\n- sS ... sequence of the entire barcode (CB,UMI,adapter).\n- sQ ... quality of the entire barcode.\n- sF ... type of feature overlap and number of features for each alignment\n***Unsupported/undocumented:\n- rB ... alignment block read/genomic coordinates.\n- vR ... read coordinate of the variant." - - } - - - , - "out_sam_attr_ih_start": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. start value for the IH attribute", - "help_text": "Type: `integer`, example: `1`. start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie." - - } - - - , - "out_sam_unmapped": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. output of unmapped reads in the SAM format\n\n1st word:\n- None ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. output of unmapped reads in the SAM format\n\n1st word:\n- None ... no output\n- Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam)\n2nd word:\n- KeepPairs ... record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects multi-mapping reads." - - } - - - , - "out_sam_order": { - "type": - "string", - "description": "Type: `string`, example: `Paired`. type of sorting for the SAM output\n\nPaired: one mate after the other for all paired alignments\nPairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files", - "help_text": "Type: `string`, example: `Paired`. type of sorting for the SAM output\n\nPaired: one mate after the other for all paired alignments\nPairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files" - - } - - - , - "out_sam_primary_flag": { - "type": - "string", - "description": "Type: `string`, example: `OneBestScore`. which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG\n\n- OneBestScore ", - "help_text": "Type: `string`, example: `OneBestScore`. which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG\n\n- OneBestScore ... only one alignment with the best score is primary\n- AllBestScore ... all alignments with the best score are primary" - - } - - - , - "out_sam_read_id": { - "type": - "string", - "description": "Type: `string`, example: `Standard`. read ID record type\n\n- Standard ", - "help_text": "Type: `string`, example: `Standard`. read ID record type\n\n- Standard ... first word (until space) from the FASTx read ID line, removing /1,/2 from the end\n- Number ... read number (index) in the FASTx file" - - } - - - , - "out_sam_mapq_unique": { - "type": - "integer", - "description": "Type: `integer`, example: `255`. 0 to 255: the MAPQ value for unique mappers", - "help_text": "Type: `integer`, example: `255`. 0 to 255: the MAPQ value for unique mappers" - - } - - - , - "out_sam_flag_or": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. 0 to 65535: sam FLAG will be bitwise OR\u0027d with this value, i", - "help_text": "Type: `integer`, example: `0`. 0 to 65535: sam FLAG will be bitwise OR\u0027d with this value, i.e. FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise." - - } - - - , - "out_sam_flag_and": { - "type": - "integer", - "description": "Type: `integer`, example: `65535`. 0 to 65535: sam FLAG will be bitwise AND\u0027d with this value, i", - "help_text": "Type: `integer`, example: `65535`. 0 to 65535: sam FLAG will be bitwise AND\u0027d with this value, i.e. FLAG=FLAG \u0026 outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise." - - } - - - , - "out_sam_attr_rg_line": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. SAM/BAM read group line", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. SAM/BAM read group line. The first word contains the read group identifier and must start with \"ID:\", e.g. --out_sam_attr_rg_line ID:xxx CN:yy \"DS:z z z\".\n\nxxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted.\nComma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g.\n--out_sam_attr_rg_line ID:xxx , ID:zzz \"DS:z z\" , ID:yyy DS:yyyy" - - } - - - , - "out_sam_header_hd": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. @HD (header) line of the SAM header", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. @HD (header) line of the SAM header" - - } - - - , - "out_sam_header_pg": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. extra @PG (software) line of the SAM header (in addition to STAR)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. extra @PG (software) line of the SAM header (in addition to STAR)" - - } - - - , - "out_sam_header_comment_file": { - "type": - "string", - "description": "Type: `string`. path to the file with @CO (comment) lines of the SAM header", - "help_text": "Type: `string`. path to the file with @CO (comment) lines of the SAM header" - - } - - - , - "out_sam_filter": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. filter the output into main SAM/BAM files\n\n- KeepOnlyAddedReferences ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. filter the output into main SAM/BAM files\n\n- KeepOnlyAddedReferences ... only keep the reads for which all alignments are to the extra reference sequences added with --genome_fasta_files at the mapping stage.\n- KeepAllAddedReferences ... keep all alignments to the extra reference sequences added with --genome_fasta_files at the mapping stage." - - } - - - , - "out_sam_mult_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. max number of multiple alignments for a read that will be output to the SAM/BAM files", - "help_text": "Type: `integer`, example: `-1`. max number of multiple alignments for a read that will be output to the SAM/BAM files. Note that if this value is not equal to -1, the top scoring alignment will be output first\n\n- -1 ... all alignments (up to --out_filter_multimap_nmax) will be output" - - } - - - , - "out_sam_tlen": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. calculation method for the TLEN field in the SAM/BAM files\n\n- 1 ", - "help_text": "Type: `integer`, example: `1`. calculation method for the TLEN field in the SAM/BAM files\n\n- 1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate\n- 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends" - - } - - - , - "out_bam_compression": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. -1 to 10 BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression", - "help_text": "Type: `integer`, example: `1`. -1 to 10 BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression" - - } - - - , - "out_bam_sorting_thread_n": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. \u003e=0: number of threads for BAM sorting", - "help_text": "Type: `integer`, example: `0`. \u003e=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN)." - - } - - - , - "out_bam_sorting_bins_n": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. \u003e0: number of genome bins for coordinate-sorting", - "help_text": "Type: `integer`, example: `50`. \u003e0: number of genome bins for coordinate-sorting" - - } - - -} -}, - - - "bam processing" : { - "title": "BAM processing", - "type": "object", - "description": "No description", - "properties": { - - - "bam_remove_duplicates_type": { - "type": - "string", - "description": "Type: `string`. mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only\n\n- - ", - "help_text": "Type: `string`. mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only\n\n- - ... no duplicate removal/marking\n- UniqueIdentical ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical\n- UniqueIdenticalNotMulti ... mark duplicate unique mappers but not multimappers." - - } - - - , - "bam_remove_duplicates_mate2bases_n": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. number of bases from the 5\u0027 of mate 2 to use in collapsing (e", - "help_text": "Type: `integer`, example: `0`. number of bases from the 5\u0027 of mate 2 to use in collapsing (e.g. for RAMPAGE)" - - } - - -} -}, - - - "output wiggle" : { - "title": "Output Wiggle", - "type": "object", - "description": "No description", - "properties": { - - - "out_wig_type": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. type of signal output, e", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. type of signal output, e.g. \"bedGraph\" OR \"bedGraph read1_5p\". Requires sorted BAM: --out_sam_type BAM SortedByCoordinate .\n\n1st word:\n- None ... no signal output\n- bedGraph ... bedGraph format\n- wiggle ... wiggle format\n2nd word:\n- read1_5p ... signal from only 5\u0027 of the 1st read, useful for CAGE/RAMPAGE etc\n- read2 ... signal from only 2nd read" - - } - - - , - "out_wig_strand": { - "type": - "string", - "description": "Type: `string`, example: `Stranded`. strandedness of wiggle/bedGraph output\n\n- Stranded ", - "help_text": "Type: `string`, example: `Stranded`. strandedness of wiggle/bedGraph output\n\n- Stranded ... separate strands, str1 and str2\n- Unstranded ... collapsed strands" - - } - - - , - "out_wig_references_prefix": { - "type": - "string", - "description": "Type: `string`. prefix matching reference names to include in the output wiggle file, e", - "help_text": "Type: `string`. prefix matching reference names to include in the output wiggle file, e.g. \"chr\", default \"-\" - include all references" - - } - - - , - "out_wig_norm": { - "type": - "string", - "description": "Type: `string`, example: `RPM`. type of normalization for the signal\n\n- RPM ", - "help_text": "Type: `string`, example: `RPM`. type of normalization for the signal\n\n- RPM ... reads per million of mapped reads\n- None ... no normalization, \"raw\" counts" - - } - - -} -}, - - - "output filtering" : { - "title": "Output Filtering", - "type": "object", - "description": "No description", - "properties": { - - - "out_filter_type": { - "type": - "string", - "description": "Type: `string`, example: `Normal`. type of filtering\n\n- Normal ", - "help_text": "Type: `string`, example: `Normal`. type of filtering\n\n- Normal ... standard filtering using only current alignment\n- BySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab" - - } - - - , - "out_filter_multimap_score_range": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. the score range below the maximum score for multimapping alignments", - "help_text": "Type: `integer`, example: `1`. the score range below the maximum score for multimapping alignments" - - } - - - , - "out_filter_multimap_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. maximum number of loci the read is allowed to map to", - "help_text": "Type: `integer`, example: `10`. maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value.\n\nOtherwise no alignments will be output, and the read will be counted as \"mapped to too many loci\" in the Log.final.out ." - - } - - - , - "out_filter_mismatch_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. alignment will be output only if it has no more mismatches than this value", - "help_text": "Type: `integer`, example: `10`. alignment will be output only if it has no more mismatches than this value." - - } - - - , - "out_filter_mismatch_nover_lmax": { - "type": - "number", - "description": "Type: `double`, example: `0.3`. alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value", - "help_text": "Type: `double`, example: `0.3`. alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value." - - } - - - , - "out_filter_mismatch_nover_read_lmax": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value", - "help_text": "Type: `double`, example: `1.0`. alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value." - - } - - - , - "out_filter_score_min": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. alignment will be output only if its score is higher than or equal to this value", - "help_text": "Type: `integer`, example: `0`. alignment will be output only if its score is higher than or equal to this value." - - } - - - , - "out_filter_score_min_over_lread": { - "type": - "number", - "description": "Type: `double`, example: `0.66`. same as outFilterScoreMin, but normalized to read length (sum of mates\u0027 lengths for paired-end reads)", - "help_text": "Type: `double`, example: `0.66`. same as outFilterScoreMin, but normalized to read length (sum of mates\u0027 lengths for paired-end reads)" - - } - - - , - "out_filter_match_nmin": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. alignment will be output only if the number of matched bases is higher than or equal to this value", - "help_text": "Type: `integer`, example: `0`. alignment will be output only if the number of matched bases is higher than or equal to this value." - - } - - - , - "out_filter_match_nmin_over_lread": { - "type": - "number", - "description": "Type: `double`, example: `0.66`. sam as outFilterMatchNmin, but normalized to the read length (sum of mates\u0027 lengths for paired-end reads)", - "help_text": "Type: `double`, example: `0.66`. sam as outFilterMatchNmin, but normalized to the read length (sum of mates\u0027 lengths for paired-end reads)." - - } - - - , - "out_filter_intron_motifs": { - "type": - "string", - "description": "Type: `string`. filter alignment using their motifs\n\n- None ", - "help_text": "Type: `string`. filter alignment using their motifs\n\n- None ... no filtering\n- RemoveNoncanonical ... filter out alignments that contain non-canonical junctions\n- RemoveNoncanonicalUnannotated ... filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept." - - } - - - , - "out_filter_intron_strands": { - "type": - "string", - "description": "Type: `string`, example: `RemoveInconsistentStrands`. filter alignments\n\n- RemoveInconsistentStrands ", - "help_text": "Type: `string`, example: `RemoveInconsistentStrands`. filter alignments\n\n- RemoveInconsistentStrands ... remove alignments that have junctions with inconsistent strands\n- None ... no filtering" - - } - - -} -}, - - - "output splice junctions (sj.out.tab)" : { - "title": "Output splice junctions (SJ.out.tab)", - "type": "object", - "description": "No description", - "properties": { - - - "out_sj_type": { - "type": - "string", - "description": "Type: `string`, example: `Standard`. type of splice junction output\n\n- Standard ", - "help_text": "Type: `string`, example: `Standard`. type of splice junction output\n\n- Standard ... standard SJ.out.tab output\n- None ... no splice junction output" - - } - - -} -}, - - - "output filtering: splice junctions" : { - "title": "Output Filtering: Splice Junctions", - "type": "object", - "description": "No description", - "properties": { - - - "out_sj_filter_reads": { - "type": - "string", - "description": "Type: `string`, example: `All`. which reads to consider for collapsed splice junctions output\n\n- All ", - "help_text": "Type: `string`, example: `All`. which reads to consider for collapsed splice junctions output\n\n- All ... all reads, unique- and multi-mappers\n- Unique ... uniquely mapping reads only" - - } - - - , - "out_sj_filter_overhang_min": { - "type": - "string", - "description": "Type: List of `integer`, example: `30;12;12;12`, multiple_sep: `\";\"`. minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", - "help_text": "Type: List of `integer`, example: `30;12;12;12`, multiple_sep: `\";\"`. minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif\n\ndoes not apply to annotated junctions" - - } - - - , - "out_sj_filter_count_unique_min": { - "type": - "string", - "description": "Type: List of `integer`, example: `3;1;1;1`, multiple_sep: `\";\"`. minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", - "help_text": "Type: List of `integer`, example: `3;1;1;1`, multiple_sep: `\";\"`. minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif\n\nJunctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied\ndoes not apply to annotated junctions" - - } - - - , - "out_sj_filter_count_total_min": { - "type": - "string", - "description": "Type: List of `integer`, example: `3;1;1;1`, multiple_sep: `\";\"`. minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", - "help_text": "Type: List of `integer`, example: `3;1;1;1`, multiple_sep: `\";\"`. minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif\n\nJunctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied\ndoes not apply to annotated junctions" - - } - - - , - "out_sj_filter_dist_to_other_sj_min": { - "type": - "string", - "description": "Type: List of `integer`, example: `10;0;5;10`, multiple_sep: `\";\"`. minimum allowed distance to other junctions\u0027 donor/acceptor\n\ndoes not apply to annotated junctions", - "help_text": "Type: List of `integer`, example: `10;0;5;10`, multiple_sep: `\";\"`. minimum allowed distance to other junctions\u0027 donor/acceptor\n\ndoes not apply to annotated junctions" - - } - - - , - "out_sj_filter_intron_max_vs_read_n": { - "type": - "string", - "description": "Type: List of `integer`, example: `50000;100000;200000`, multiple_sep: `\";\"`. maximum gap allowed for junctions supported by 1,2,3,,,N reads\n\ni", - "help_text": "Type: List of `integer`, example: `50000;100000;200000`, multiple_sep: `\";\"`. maximum gap allowed for junctions supported by 1,2,3,,,N reads\n\ni.e. by default junctions supported by 1 read can have gaps \u003c=50000b, by 2 reads: \u003c=100000b, by 3 reads: \u003c=200000. by \u003e=4 reads any gap \u003c=alignIntronMax\ndoes not apply to annotated junctions" - - } - - -} -}, - - - "scoring" : { - "title": "Scoring", - "type": "object", - "description": "No description", - "properties": { - - - "score_gap": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. splice junction penalty (independent on intron motif)", - "help_text": "Type: `integer`, example: `0`. splice junction penalty (independent on intron motif)" - - } - - - , - "score_gap_noncan": { - "type": - "integer", - "description": "Type: `integer`, example: `-8`. non-canonical junction penalty (in addition to scoreGap)", - "help_text": "Type: `integer`, example: `-8`. non-canonical junction penalty (in addition to scoreGap)" - - } - - - , - "score_gap_gcag": { - "type": - "integer", - "description": "Type: `integer`, example: `-4`. GC/AG and CT/GC junction penalty (in addition to scoreGap)", - "help_text": "Type: `integer`, example: `-4`. GC/AG and CT/GC junction penalty (in addition to scoreGap)" - - } - - - , - "score_gap_atac": { - "type": - "integer", - "description": "Type: `integer`, example: `-8`. AT/AC and GT/AT junction penalty (in addition to scoreGap)", - "help_text": "Type: `integer`, example: `-8`. AT/AC and GT/AT junction penalty (in addition to scoreGap)" - - } - - - , - "score_genomic_length_log2scale": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)", - "help_text": "Type: `integer`, example: `0`. extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)" - - } - - - , - "score_del_open": { - "type": - "integer", - "description": "Type: `integer`, example: `-2`. deletion open penalty", - "help_text": "Type: `integer`, example: `-2`. deletion open penalty" - - } - - - , - "score_del_base": { - "type": - "integer", - "description": "Type: `integer`, example: `-2`. deletion extension penalty per base (in addition to scoreDelOpen)", - "help_text": "Type: `integer`, example: `-2`. deletion extension penalty per base (in addition to scoreDelOpen)" - - } - - - , - "score_ins_open": { - "type": - "integer", - "description": "Type: `integer`, example: `-2`. insertion open penalty", - "help_text": "Type: `integer`, example: `-2`. insertion open penalty" - - } - - - , - "score_ins_base": { - "type": - "integer", - "description": "Type: `integer`, example: `-2`. insertion extension penalty per base (in addition to scoreInsOpen)", - "help_text": "Type: `integer`, example: `-2`. insertion extension penalty per base (in addition to scoreInsOpen)" - - } - - - , - "score_stitch_sj_shift": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. maximum score reduction while searching for SJ boundaries in the stitching step", - "help_text": "Type: `integer`, example: `1`. maximum score reduction while searching for SJ boundaries in the stitching step" - - } - - -} -}, - - - "alignments and seeding" : { - "title": "Alignments and Seeding", - "type": "object", - "description": "No description", - "properties": { - - - "seed_search_start_lmax": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. defines the search start point through the read - the read is split into pieces no longer than this value", - "help_text": "Type: `integer`, example: `50`. defines the search start point through the read - the read is split into pieces no longer than this value" - - } - - - , - "seed_search_start_lmax_over_lread": { - "type": - "number", - "description": "Type: `double`, example: `1.0`. seedSearchStartLmax normalized to read length (sum of mates\u0027 lengths for paired-end reads)", - "help_text": "Type: `double`, example: `1.0`. seedSearchStartLmax normalized to read length (sum of mates\u0027 lengths for paired-end reads)" - - } - - - , - "seed_search_lmax": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. defines the maximum length of the seeds, if =0 seed length is not limited", - "help_text": "Type: `integer`, example: `0`. defines the maximum length of the seeds, if =0 seed length is not limited" - - } - - - , - "seed_multimap_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. only pieces that map fewer than this value are utilized in the stitching procedure", - "help_text": "Type: `integer`, example: `10000`. only pieces that map fewer than this value are utilized in the stitching procedure" - - } - - - , - "seed_per_read_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `1000`. max number of seeds per read", - "help_text": "Type: `integer`, example: `1000`. max number of seeds per read" - - } - - - , - "seed_per_window_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. max number of seeds per window", - "help_text": "Type: `integer`, example: `50`. max number of seeds per window" - - } - - - , - "seed_none_loci_per_window": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. max number of one seed loci per window", - "help_text": "Type: `integer`, example: `10`. max number of one seed loci per window" - - } - - - , - "seed_split_min": { - "type": - "integer", - "description": "Type: `integer`, example: `12`. min length of the seed sequences split by Ns or mate gap", - "help_text": "Type: `integer`, example: `12`. min length of the seed sequences split by Ns or mate gap" - - } - - - , - "seed_map_min": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. min length of seeds to be mapped", - "help_text": "Type: `integer`, example: `5`. min length of seeds to be mapped" - - } - - - , - "align_intron_min": { - "type": - "integer", - "description": "Type: `integer`, example: `21`. minimum intron size, genomic gap is considered intron if its length\u003e=alignIntronMin, otherwise it is considered Deletion", - "help_text": "Type: `integer`, example: `21`. minimum intron size, genomic gap is considered intron if its length\u003e=alignIntronMin, otherwise it is considered Deletion" - - } - - - , - "align_intron_max": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins", - "help_text": "Type: `integer`, example: `0`. maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins" - - } - - - , - "align_mates_gap_max": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins", - "help_text": "Type: `integer`, example: `0`. maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins" - - } - - - , - "align_sj_overhang_min": { - "type": - "integer", - "description": "Type: `integer`, example: `5`. minimum overhang (i", - "help_text": "Type: `integer`, example: `5`. minimum overhang (i.e. block size) for spliced alignments" - - } - - - , - "align_sj_stitch_mismatch_nmax": { - "type": - "string", - "description": "Type: List of `integer`, example: `0;-1;0;0`, multiple_sep: `\";\"`. maximum number of mismatches for stitching of the splice junctions (-1: no limit)", - "help_text": "Type: List of `integer`, example: `0;-1;0;0`, multiple_sep: `\";\"`. maximum number of mismatches for stitching of the splice junctions (-1: no limit).\n\n(1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif." - - } - - - , - "align_sjdb_overhang_min": { - "type": - "integer", - "description": "Type: `integer`, example: `3`. minimum overhang (i", - "help_text": "Type: `integer`, example: `3`. minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments" - - } - - - , - "align_spliced_mate_map_lmin": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. minimum mapped length for a read mate that is spliced", - "help_text": "Type: `integer`, example: `0`. minimum mapped length for a read mate that is spliced" - - } - - - , - "align_spliced_mate_map_lmin_over_lmate": { - "type": - "number", - "description": "Type: `double`, example: `0.66`. alignSplicedMateMapLmin normalized to mate length", - "help_text": "Type: `double`, example: `0.66`. alignSplicedMateMapLmin normalized to mate length" - - } - - - , - "align_windows_per_read_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. max number of windows per read", - "help_text": "Type: `integer`, example: `10000`. max number of windows per read" - - } - - - , - "align_transcripts_per_window_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. max number of transcripts per window", - "help_text": "Type: `integer`, example: `100`. max number of transcripts per window" - - } - - - , - "align_transcripts_per_read_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10000`. max number of different alignments per read to consider", - "help_text": "Type: `integer`, example: `10000`. max number of different alignments per read to consider" - - } - - - , - "align_ends_type": { - "type": - "string", - "description": "Type: `string`, example: `Local`. type of read ends alignment\n\n- Local ", - "help_text": "Type: `string`, example: `Local`. type of read ends alignment\n\n- Local ... standard local alignment with soft-clipping allowed\n- EndToEnd ... force end-to-end read alignment, do not soft-clip\n- Extend5pOfRead1 ... fully extend only the 5p of the read1, all other ends: local alignment\n- Extend5pOfReads12 ... fully extend only the 5p of the both read1 and read2, all other ends: local alignment" - - } - - - , - "align_ends_protrude": { - "type": - "string", - "description": "Type: `string`, example: `0 ConcordantPair`. allow protrusion of alignment ends, i", - "help_text": "Type: `string`, example: `0 ConcordantPair`. allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate\n\n1st word: int: maximum number of protrusion bases allowed\n2nd word: string:\n- ConcordantPair ... report alignments with non-zero protrusion as concordant pairs\n- DiscordantPair ... report alignments with non-zero protrusion as discordant pairs" - - } - - - , - "align_soft_clip_at_reference_ends": { - "type": - "string", - "description": "Type: `string`, example: `Yes`. allow the soft-clipping of the alignments past the end of the chromosomes\n\n- Yes ", - "help_text": "Type: `string`, example: `Yes`. allow the soft-clipping of the alignments past the end of the chromosomes\n\n- Yes ... allow\n- No ... prohibit, useful for compatibility with Cufflinks" - - } - - - , - "align_insertion_flush": { - "type": - "string", - "description": "Type: `string`. how to flush ambiguous insertion positions\n\n- None ", - "help_text": "Type: `string`. how to flush ambiguous insertion positions\n\n- None ... insertions are not flushed\n- Right ... insertions are flushed to the right" - - } - - -} -}, - - - "paired-end reads" : { - "title": "Paired-End reads", - "type": "object", - "description": "No description", - "properties": { - - - "pe_overlap_nbases_min": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. minimum number of overlapping bases to trigger mates merging and realignment", - "help_text": "Type: `integer`, example: `0`. minimum number of overlapping bases to trigger mates merging and realignment. Specify \u003e0 value to switch on the \"merginf of overlapping mates\" algorithm." - - } - - - , - "pe_overlap_mm_p": { - "type": - "number", - "description": "Type: `double`, example: `0.01`. maximum proportion of mismatched bases in the overlap area", - "help_text": "Type: `double`, example: `0.01`. maximum proportion of mismatched bases in the overlap area" - - } - - -} -}, - - - "windows, anchors, binning" : { - "title": "Windows, Anchors, Binning", - "type": "object", - "description": "No description", - "properties": { - - - "win_anchor_multimap_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `50`. max number of loci anchors are allowed to map to", - "help_text": "Type: `integer`, example: `50`. max number of loci anchors are allowed to map to" - - } - - - , - "win_bin_nbits": { - "type": - "integer", - "description": "Type: `integer`, example: `16`. =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins", - "help_text": "Type: `integer`, example: `16`. =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins." - - } - - - , - "win_anchor_dist_nbins": { - "type": - "integer", - "description": "Type: `integer`, example: `9`. max number of bins between two anchors that allows aggregation of anchors into one window", - "help_text": "Type: `integer`, example: `9`. max number of bins between two anchors that allows aggregation of anchors into one window" - - } - - - , - "win_flank_nbins": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. log2(winFlank), where win Flank is the size of the left and right flanking regions for each window", - "help_text": "Type: `integer`, example: `4`. log2(winFlank), where win Flank is the size of the left and right flanking regions for each window" - - } - - - , - "win_read_coverage_relative_min": { - "type": - "number", - "description": "Type: `double`, example: `0.5`. minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only", - "help_text": "Type: `double`, example: `0.5`. minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only." - - } - - - , - "win_read_coverage_bases_min": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. minimum number of bases covered by the seeds in a window , for STARlong algorithm only", - "help_text": "Type: `integer`, example: `0`. minimum number of bases covered by the seeds in a window , for STARlong algorithm only." - - } - - -} -}, - - - "chimeric alignments" : { - "title": "Chimeric Alignments", - "type": "object", - "description": "No description", - "properties": { - - - "chim_out_type": { - "type": - "string", - "description": "Type: List of `string`, example: `Junctions`, multiple_sep: `\";\"`. type of chimeric output\n\n- Junctions ", - "help_text": "Type: List of `string`, example: `Junctions`, multiple_sep: `\";\"`. type of chimeric output\n\n- Junctions ... Chimeric.out.junction\n- SeparateSAMold ... output old SAM into separate Chimeric.out.sam file\n- WithinBAM ... output into main aligned BAM files (Aligned.*.bam)\n- WithinBAM HardClip ... (default) hard-clipping in the CIGAR for supplemental chimeric alignments (default if no 2nd word is present)\n- WithinBAM SoftClip ... soft-clipping in the CIGAR for supplemental chimeric alignments" - - } - - - , - "chim_segment_min": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. minimum length of chimeric segment length, if ==0, no chimeric output", - "help_text": "Type: `integer`, example: `0`. minimum length of chimeric segment length, if ==0, no chimeric output" - - } - - - , - "chim_score_min": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. minimum total (summed) score of the chimeric segments", - "help_text": "Type: `integer`, example: `0`. minimum total (summed) score of the chimeric segments" - - } - - - , - "chim_score_drop_max": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length", - "help_text": "Type: `integer`, example: `20`. max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length" - - } - - - , - "chim_score_separation": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. minimum difference (separation) between the best chimeric score and the next one", - "help_text": "Type: `integer`, example: `10`. minimum difference (separation) between the best chimeric score and the next one" - - } - - - , - "chim_score_junction_non_gtag": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. penalty for a non-GT/AG chimeric junction", - "help_text": "Type: `integer`, example: `-1`. penalty for a non-GT/AG chimeric junction" - - } - - - , - "chim_junction_overhang_min": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. minimum overhang for a chimeric junction", - "help_text": "Type: `integer`, example: `20`. minimum overhang for a chimeric junction" - - } - - - , - "chim_segment_read_gap_max": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. maximum gap in the read sequence between chimeric segments", - "help_text": "Type: `integer`, example: `0`. maximum gap in the read sequence between chimeric segments" - - } - - - , - "chim_filter": { - "type": - "string", - "description": "Type: List of `string`, example: `banGenomicN`, multiple_sep: `\";\"`. different filters for chimeric alignments\n\n- None ", - "help_text": "Type: List of `string`, example: `banGenomicN`, multiple_sep: `\";\"`. different filters for chimeric alignments\n\n- None ... no filtering\n- banGenomicN ... Ns are not allowed in the genome sequence around the chimeric junction" - - } - - - , - "chim_main_segment_mult_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. maximum number of multi-alignments for the main chimeric segment", - "help_text": "Type: `integer`, example: `10`. maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments." - - } - - - , - "chim_multimap_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. maximum number of chimeric multi-alignments\n\n- 0 ", - "help_text": "Type: `integer`, example: `0`. maximum number of chimeric multi-alignments\n\n- 0 ... use the old scheme for chimeric detection which only considered unique alignments" - - } - - - , - "chim_multimap_score_range": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. the score range for multi-mapping chimeras below the best chimeric score", - "help_text": "Type: `integer`, example: `1`. the score range for multi-mapping chimeras below the best chimeric score. Only works with --chim_multimap_nmax \u003e 1" - - } - - - , - "chim_nonchim_score_drop_min": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value", - "help_text": "Type: `integer`, example: `20`. to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value" - - } - - - , - "chim_out_junction_format": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. formatting type for the Chimeric", - "help_text": "Type: `integer`, example: `0`. formatting type for the Chimeric.out.junction file\n\n- 0 ... no comment lines/headers\n- 1 ... comment lines at the end of the file: command line and Nreads: total, unique/multi-mapping" - - } - - -} -}, - - - "quantification of annotations" : { - "title": "Quantification of Annotations", - "type": "object", - "description": "No description", - "properties": { - - - "quant_mode": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. types of quantification requested\n\n- - ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. types of quantification requested\n\n- - ... none\n- TranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a separate file\n- GeneCounts ... count reads per gene" - - } - - - , - "quant_transcriptome_bam_compression": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. -2 to 10 transcriptome BAM compression level\n\n- -2 ", - "help_text": "Type: `integer`, example: `1`. -2 to 10 transcriptome BAM compression level\n\n- -2 ... no BAM output\n- -1 ... default compression (6?)\n- 0 ... no compression\n- 10 ... maximum compression" - - } - - - , - "quant_transcriptome_sam_output": { - "type": - "string", - "description": "Type: `string`, example: `BanSingleEnd_BanIndels_ExtendSoftclip`. alignment filtering for TranscriptomeSAM output\n\n- BanSingleEnd_BanIndels_ExtendSoftclip ", - "help_text": "Type: `string`, example: `BanSingleEnd_BanIndels_ExtendSoftclip`. alignment filtering for TranscriptomeSAM output\n\n- BanSingleEnd_BanIndels_ExtendSoftclip ... prohibit indels and single-end alignments, extend softclips - compatible with RSEM\n- BanSingleEnd ... prohibit single-end alignments, allow indels and softclips\n- BanSingleEnd_ExtendSoftclip ... prohibit single-end alignments, extend softclips, allow indels" - - } - - -} -}, - - - "2-pass mapping" : { - "title": "2-pass Mapping", - "type": "object", - "description": "No description", - "properties": { - - - "twopass_mode": { - "type": - "string", - "description": "Type: `string`. 2-pass mapping mode", - "help_text": "Type: `string`. 2-pass mapping mode.\n\n- None ... 1-pass mapping\n- Basic ... basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly" - - } - - - , - "twopass1reads_n": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. number of reads to process for the 1st step", - "help_text": "Type: `integer`, example: `-1`. number of reads to process for the 1st step. Use very large number (or default -1) to map all reads in the first step." - - } - - -} -}, - - - "wasp parameters" : { - "title": "WASP parameters", - "type": "object", - "description": "No description", - "properties": { - - - "wasp_output_mode": { - "type": - "string", - "description": "Type: `string`. WASP allele-specific output type", - "help_text": "Type: `string`. WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad \u0026 Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061-1063 (2015), https://www.nature.com/articles/nmeth.3582 .\n\n- SAMtag ... add WASP tags to the alignments that pass WASP filtering" - - } - - -} -}, - - - "starsolo (single cell rna-seq) parameters" : { - "title": "STARsolo (single cell RNA-seq) parameters", - "type": "object", - "description": "No description", - "properties": { - - - "solo_type": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. type of single-cell RNA-seq\n\n- CB_UMI_Simple ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. type of single-cell RNA-seq\n\n- CB_UMI_Simple ... (a.k.a. Droplet) one UMI and one Cell Barcode of fixed length in read2, e.g. Drop-seq and 10X Chromium.\n- CB_UMI_Complex ... multiple Cell Barcodes of varying length, one UMI of fixed length and one adapter sequence of fixed length are allowed in read2 only (e.g. inDrop, ddSeq).\n- CB_samTagOut ... output Cell Barcode as CR and/or CB SAm tag. No UMI counting. --readFilesIn cDNA_read1 [cDNA_read2 if paired-end] CellBarcode_read . Requires --out_sam_type BAM Unsorted [and/or SortedByCoordinate]\n- SmartSeq ... Smart-seq: each cell in a separate FASTQ (paired- or single-end), barcodes are corresponding read-groups, no UMI sequences, alignments deduplicated according to alignment start and end (after extending soft-clipped bases)" - - } - - - , - "solo_cb_type": { - "type": - "string", - "description": "Type: `string`, example: `Sequence`. cell barcode type\n\nSequence: cell barcode is a sequence (standard option)\nString: cell barcode is an arbitrary string", - "help_text": "Type: `string`, example: `Sequence`. cell barcode type\n\nSequence: cell barcode is a sequence (standard option)\nString: cell barcode is an arbitrary string" - - } - - - , - "solo_cb_whitelist": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. file(s) with whitelist(s) of cell barcodes", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. file(s) with whitelist(s) of cell barcodes. Only --solo_type CB_UMI_Complex allows more than one whitelist file.\n\n- None ... no whitelist: all cell barcodes are allowed" - - } - - - , - "solo_cb_start": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. cell barcode start base", - "help_text": "Type: `integer`, example: `1`. cell barcode start base" - - } - - - , - "solo_cb_len": { - "type": - "integer", - "description": "Type: `integer`, example: `16`. cell barcode length", - "help_text": "Type: `integer`, example: `16`. cell barcode length" - - } - - - , - "solo_umi_start": { - "type": - "integer", - "description": "Type: `integer`, example: `17`. UMI start base", - "help_text": "Type: `integer`, example: `17`. UMI start base" - - } - - - , - "solo_umi_len": { - "type": - "integer", - "description": "Type: `integer`, example: `10`. UMI length", - "help_text": "Type: `integer`, example: `10`. UMI length" - - } - - - , - "solo_barcode_read_length": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. length of the barcode read\n\n- 1 ", - "help_text": "Type: `integer`, example: `1`. length of the barcode read\n\n- 1 ... equal to sum of soloCBlen+soloUMIlen\n- 0 ... not defined, do not check" - - } - - - , - "solo_barcode_mate": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. identifies which read mate contains the barcode (CB+UMI) sequence\n\n- 0 ", - "help_text": "Type: `integer`, example: `0`. identifies which read mate contains the barcode (CB+UMI) sequence\n\n- 0 ... barcode sequence is on separate read, which should always be the last file in the --readFilesIn listed\n- 1 ... barcode sequence is a part of mate 1\n- 2 ... barcode sequence is a part of mate 2" - - } - - - , - "solo_cb_position": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. position of Cell Barcode(s) on the barcode read", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. position of Cell Barcode(s) on the barcode read.\n\nPresently only works with --solo_type CB_UMI_Complex, and barcodes are assumed to be on Read2.\nFormat for each barcode: startAnchor_startPosition_endAnchor_endPosition\nstart(end)Anchor defines the Anchor Base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end\nstart(end)Position is the 0-based position with of the CB start(end) with respect to the Anchor Base\nString for different barcodes are separated by space.\nExample: inDrop (Zilionis et al, Nat. Protocols, 2017):\n--solo_cb_position 0_0_2_-1 3_1_3_8" - - } - - - , - "solo_umi_position": { - "type": - "string", - "description": "Type: `string`. position of the UMI on the barcode read, same as soloCBposition\n\nExample: inDrop (Zilionis et al, Nat", - "help_text": "Type: `string`. position of the UMI on the barcode read, same as soloCBposition\n\nExample: inDrop (Zilionis et al, Nat. Protocols, 2017):\n--solo_cb_position 3_9_3_14" - - } - - - , - "solo_adapter_sequence": { - "type": - "string", - "description": "Type: `string`. adapter sequence to anchor barcodes", - "help_text": "Type: `string`. adapter sequence to anchor barcodes. Only one adapter sequence is allowed." - - } - - - , - "solo_adapter_mismatches_nmax": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. maximum number of mismatches allowed in adapter sequence", - "help_text": "Type: `integer`, example: `1`. maximum number of mismatches allowed in adapter sequence." - - } - - - , - "solo_cb_match_wl_type": { - "type": - "string", - "description": "Type: `string`, example: `1MM_multi`. matching the Cell Barcodes to the WhiteList\n\n- Exact ", - "help_text": "Type: `string`, example: `1MM_multi`. matching the Cell Barcodes to the WhiteList\n\n- Exact ... only exact matches allowed\n- 1MM ... only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match.\n- 1MM_multi ... multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches.\nAllowed CBs have to have at least one read with exact match. This option matches best with CellRanger 2.2.0\n- 1MM_multi_pseudocounts ... same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes.\n- 1MM_multi_Nbase_pseudocounts ... same as 1MM_multi_pseudocounts, multimatching to WL is allowed for CBs with N-bases. This option matches best with CellRanger \u003e= 3.0.0\n- EditDist_2 ... allow up to edit distance of 3 fpr each of the barcodes. May include one deletion + one insertion. Only works with --solo_type CB_UMI_Complex. Matches to multiple passlist barcdoes are not allowed. Similar to ParseBio Split-seq pipeline." - - } - - - , - "solo_input_sam_attr_barcode_seq": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode sequence (in proper order)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode sequence (in proper order).\n\nFor instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_seq CR UR .\nThis parameter is required when running STARsolo with input from SAM." - - } - - - , - "solo_input_sam_attr_barcode_qual": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode qualities (in proper order)", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode qualities (in proper order).\n\nFor instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_qual CY UY .\nIf this parameter is \u0027-\u0027 (default), the quality \u0027H\u0027 will be assigned to all bases." - - } - - - , - "solo_strand": { - "type": - "string", - "description": "Type: `string`, example: `Forward`. strandedness of the solo libraries:\n\n- Unstranded ", - "help_text": "Type: `string`, example: `Forward`. strandedness of the solo libraries:\n\n- Unstranded ... no strand information\n- Forward ... read strand same as the original RNA molecule\n- Reverse ... read strand opposite to the original RNA molecule" - - } - - - , - "solo_features": { - "type": - "string", - "description": "Type: List of `string`, example: `Gene`, multiple_sep: `\";\"`. genomic features for which the UMI counts per Cell Barcode are collected\n\n- Gene ", - "help_text": "Type: List of `string`, example: `Gene`, multiple_sep: `\";\"`. genomic features for which the UMI counts per Cell Barcode are collected\n\n- Gene ... genes: reads match the gene transcript\n- SJ ... splice junctions: reported in SJ.out.tab\n- GeneFull ... full gene (pre-mRNA): count all reads overlapping genes\u0027 exons and introns\n- GeneFull_ExonOverIntron ... full gene (pre-mRNA): count all reads overlapping genes\u0027 exons and introns: prioritize 100% overlap with exons\n- GeneFull_Ex50pAS ... full gene (pre-RNA): count all reads overlapping genes\u0027 exons and introns: prioritize \u003e50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction." - - } - - - , - "solo_multi_mappers": { - "type": - "string", - "description": "Type: List of `string`, example: `Unique`, multiple_sep: `\";\"`. counting method for reads mapping to multiple genes\n\n- Unique ", - "help_text": "Type: List of `string`, example: `Unique`, multiple_sep: `\";\"`. counting method for reads mapping to multiple genes\n\n- Unique ... count only reads that map to unique genes\n- Uniform ... uniformly distribute multi-genic UMIs to all genes\n- Rescue ... distribute UMIs proportionally to unique+uniform counts (~ first iteration of EM)\n- PropUnique ... distribute UMIs proportionally to unique mappers, if present, and uniformly if not.\n- EM ... multi-gene UMIs are distributed using Expectation Maximization algorithm" - - } - - - , - "solo_umi_dedup": { - "type": - "string", - "description": "Type: List of `string`, example: `1MM_All`, multiple_sep: `\";\"`. type of UMI deduplication (collapsing) algorithm\n\n- 1MM_All ", - "help_text": "Type: List of `string`, example: `1MM_All`, multiple_sep: `\";\"`. type of UMI deduplication (collapsing) algorithm\n\n- 1MM_All ... all UMIs with 1 mismatch distance to each other are collapsed (i.e. counted once).\n- 1MM_Directional_UMItools ... follows the \"directional\" method from the UMI-tools by Smith, Heger and Sudbery (Genome Research 2017).\n- 1MM_Directional ... same as 1MM_Directional_UMItools, but with more stringent criteria for duplicate UMIs\n- Exact ... only exactly matching UMIs are collapsed.\n- NoDedup ... no deduplication of UMIs, count all reads.\n- 1MM_CR ... CellRanger2-4 algorithm for 1MM UMI collapsing." - - } - - - , - "solo_umi_filtering": { - "type": - "string", - "description": "Type: List of `string`, multiple_sep: `\";\"`. type of UMI filtering (for reads uniquely mapping to genes)\n\n- - ", - "help_text": "Type: List of `string`, multiple_sep: `\";\"`. type of UMI filtering (for reads uniquely mapping to genes)\n\n- - ... basic filtering: remove UMIs with N and homopolymers (similar to CellRanger 2.2.0).\n- MultiGeneUMI ... basic + remove lower-count UMIs that map to more than one gene.\n- MultiGeneUMI_All ... basic + remove all UMIs that map to more than one gene.\n- MultiGeneUMI_CR ... basic + remove lower-count UMIs that map to more than one gene, matching CellRanger \u003e 3.0.0 .\nOnly works with --solo_umi_dedup 1MM_CR" - - } - - - , - "solo_out_file_names": { - "type": - "string", - "description": "Type: List of `string`, example: `Solo.out/;features.tsv;barcodes.tsv;matrix.mtx`, multiple_sep: `\";\"`. file names for STARsolo output:\n\nfile_name_prefix gene_names barcode_sequences cell_feature_count_matrix", - "help_text": "Type: List of `string`, example: `Solo.out/;features.tsv;barcodes.tsv;matrix.mtx`, multiple_sep: `\";\"`. file names for STARsolo output:\n\nfile_name_prefix gene_names barcode_sequences cell_feature_count_matrix" - - } - - - , - "solo_cell_filter": { - "type": - "string", - "description": "Type: List of `string`, example: `CellRanger2.2;3000;0.99;10`, multiple_sep: `\";\"`. cell filtering type and parameters\n\n- None ", - "help_text": "Type: List of `string`, example: `CellRanger2.2;3000;0.99;10`, multiple_sep: `\";\"`. cell filtering type and parameters\n\n- None ... do not output filtered cells\n- TopCells ... only report top cells by UMI count, followed by the exact number of cells\n- CellRanger2.2 ... simple filtering of CellRanger 2.2.\nCan be followed by numbers: number of expected cells, robust maximum percentile for UMI count, maximum to minimum ratio for UMI count\nThe harcoded values are from CellRanger: nExpectedCells=3000; maxPercentile=0.99; maxMinRatio=10\n- EmptyDrops_CR ... EmptyDrops filtering in CellRanger flavor. Please cite the original EmptyDrops paper: A.T.L Lun et al, Genome Biology, 20, 63 (2019): https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1662-y\nCan be followed by 10 numeric parameters: nExpectedCells maxPercentile maxMinRatio indMin indMax umiMin umiMinFracMedian candMaxN FDR simN\nThe harcoded values are from CellRanger: 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000" - - } - - - , - "solo_out_format_features_gene_field3": { - "type": - "string", - "description": "Type: List of `string`, example: `Gene Expression`, multiple_sep: `\";\"`. field 3 in the Gene features", - "help_text": "Type: List of `string`, example: `Gene Expression`, multiple_sep: `\";\"`. field 3 in the Gene features.tsv file. If \"-\", then no 3rd field is output." - - } - - - , - "solo_cell_read_stats": { - "type": - "string", - "description": "Type: `string`. Output reads statistics for each CB\n\n- Standard ", - "help_text": "Type: `string`. Output reads statistics for each CB\n\n- Standard ... standard output" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "star_align_reads", + "description": "Aligns reads to a reference genome using STAR.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "The single-end or paired-end R1 FastQ files to be processed.", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"mysample_S1_L001_R1_001.fastq.gz\"]`. " + }, + "input_r2": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "The paired-end R2 FastQ files to be processed", + "help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"mysample_S1_L001_R2_001.fastq.gz\"]`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "aligned_reads": { + "type": "string", + "format": "path", + "description": "The output file containing the aligned reads.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.aligned_reads.bam\"`, direction: `output`, example: `\"aligned_reads.bam\"`. ", + "default": "$id.$key.aligned_reads.bam" + }, + "reads_per_gene": { + "type": "string", + "format": "path", + "description": "The output file containing the number of reads per gene.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.reads_per_gene.tsv\"`, direction: `output`, example: `\"reads_per_gene.tsv\"`. ", + "default": "$id.$key.reads_per_gene.tsv" + }, + "unmapped": { + "type": "string", + "format": "path", + "description": "The output file containing the unmapped reads.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unmapped.fastq\"`, direction: `output`, example: `\"unmapped.fastq\"`. ", + "default": "$id.$key.unmapped.fastq" + }, + "unmapped_r2": { + "type": "string", + "format": "path", + "description": "The output file containing the unmapped R2 reads.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unmapped_r2.fastq\"`, direction: `output`, example: `\"unmapped_r2.fastq\"`. ", + "default": "$id.$key.unmapped_r2.fastq" + }, + "chimeric_junctions": { + "type": "string", + "format": "path", + "description": "The output file containing the chimeric junctions.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.chimeric_junctions.tsv\"`, direction: `output`, example: `\"chimeric_junctions.tsv\"`. ", + "default": "$id.$key.chimeric_junctions.tsv" + }, + "log": { + "type": "string", + "format": "path", + "description": "The output file containing the log of the alignment process.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log.txt\"`, direction: `output`, example: `\"log.txt\"`. ", + "default": "$id.$key.log.txt" + }, + "splice_junctions": { + "type": "string", + "format": "path", + "description": "The output file containing the splice junctions.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.splice_junctions.tsv\"`, direction: `output`, example: `\"splice_junctions.tsv\"`. ", + "default": "$id.$key.splice_junctions.tsv" + }, + "reads_aligned_to_transcriptome": { + "type": "string", + "format": "path", + "description": "The output file containing the alignments to transcriptome in BAM formats", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.reads_aligned_to_transcriptome.bam\"`, direction: `output`, example: `\"transcriptome_aligned.bam\"`. ", + "default": "$id.$key.reads_aligned_to_transcriptome.bam" + } + } }, - - { - "$ref": "#/definitions/run parameters" + "run parameters": { + "title": "Run Parameters", + "type": "object", + "description": "No description", + "properties": { + "run_rng_seed": { + "type": "integer", + "description": "random number generator seed.", + "help_text": "Type: `integer`, multiple: `False`, example: `777`. " + } + } }, - - { - "$ref": "#/definitions/genome parameters" + "genome parameters": { + "title": "Genome Parameters", + "type": "object", + "description": "No description", + "properties": { + "genome_dir": { + "type": "string", + "format": "path", + "exists": true, + "description": "path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome)", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"./GenomeDir\"`. " + }, + "genome_load": { + "type": "string", + "description": "mode of shared memory usage for the genome files", + "help_text": "Type: `string`, multiple: `False`, example: `\"NoSharedMemory\"`. " + }, + "genome_fasta_files": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "description": "path(s) to the fasta files with the genome sequences, separated by spaces", + "help_text": "Type: `file`, multiple: `True`, direction: `input`. " + }, + "genome_file_sizes": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "genome files exact sizes in bytes", + "help_text": "Type: `integer`, multiple: `True`, example: `[0]`. " + }, + "genome_transform_output": { + "type": "array", + "items": { + "type": "string" + }, + "description": "which output to transform back to original genome\n\n- SAM ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "genome_chr_set_mitochondrial": { + "type": "array", + "items": { + "type": "string" + }, + "description": "names of the mitochondrial chromosomes", + "help_text": "Type: `string`, multiple: `True`, example: `[\"chrM\";\"M\";\"MT\"]`. " + } + } }, - - { - "$ref": "#/definitions/splice junctions database" + "splice junctions database": { + "title": "Splice Junctions Database", + "type": "object", + "description": "No description", + "properties": { + "sjdb_file_chr_start_end": { + "type": "array", + "items": { + "type": "string" + }, + "description": "path to the files with genomic coordinates (chr start end strand) for the splice junction introns", + "help_text": "Type: `string`, multiple: `True`. " + }, + "sjdb_gtf_file": { + "type": "string", + "format": "path", + "description": "path to the GTF file with annotations", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "sjdb_gtf_chr_prefix": { + "type": "string", + "description": "prefix for chromosome names in a GTF file (e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "sjdb_gtf_feature_exon": { + "type": "string", + "description": "feature type in GTF file to be used as exons for building transcripts", + "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. " + }, + "sjdb_gtf_tag_exon_parent_transcript": { + "type": "string", + "description": "GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)", + "help_text": "Type: `string`, multiple: `False`, example: `\"transcript_id\"`. " + }, + "sjdb_gtf_tag_exon_parent_gene": { + "type": "string", + "description": "GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)", + "help_text": "Type: `string`, multiple: `False`, example: `\"gene_id\"`. " + }, + "sjdb_gtf_tag_exon_parent_gene_name": { + "type": "array", + "items": { + "type": "string" + }, + "description": "GTF attribute name for parent gene name", + "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_name\"]`. " + }, + "sjdb_gtf_tag_exon_parent_gene_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "GTF attribute name for parent gene type", + "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_type\";\"gene_biotype\"]`. " + }, + "sjdb_overhang": { + "type": "integer", + "description": "length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "sjdb_score": { + "type": "integer", + "description": "extra alignment score for alignments that cross database junctions", + "help_text": "Type: `integer`, multiple: `False`, example: `2`. " + }, + "sjdb_insert_save": { + "type": "string", + "description": "which files to save when sjdb junctions are inserted on the fly at the mapping step\n\n- Basic ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Basic\"`. " + } + } }, - - { - "$ref": "#/definitions/variation parameters" + "variation parameters": { + "title": "Variation parameters", + "type": "object", + "description": "No description", + "properties": { + "var_vcf_file": { + "type": "string", + "description": "path to the VCF file that contains variation data", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/read parameters" + "read parameters": { + "title": "Read Parameters", + "type": "object", + "description": "No description", + "properties": { + "read_files_type": { + "type": "string", + "description": "format of input read files\n\n- Fastx ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Fastx\"`. " + }, + "read_files_sam_attr_keep": { + "type": "array", + "items": { + "type": "string" + }, + "description": "for --read_files_type SAM SE/PE, which SAM tags to keep in the output BAM, e.g.: --readFilesSAMtagsKeep RG PL\n\n- All ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"All\"]`. " + }, + "read_files_manifest": { + "type": "string", + "format": "path", + "description": "path to the \"manifest\" file with the names of read files", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "read_files_prefix": { + "type": "string", + "description": "prefix for the read files names, i.e", + "help_text": "Type: `string`, multiple: `False`. " + }, + "read_files_command": { + "type": "array", + "items": { + "type": "string" + }, + "description": "command line to execute for each of the input file", + "help_text": "Type: `string`, multiple: `True`. " + }, + "read_map_number": { + "type": "integer", + "description": "number of reads to map from the beginning of the file\n\n-1: map all reads", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "read_mates_lengths_in": { + "type": "string", + "description": "Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same", + "help_text": "Type: `string`, multiple: `False`, example: `\"NotEqual\"`. " + }, + "read_name_separator": { + "type": "array", + "items": { + "type": "string" + }, + "description": "character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)", + "help_text": "Type: `string`, multiple: `True`, example: `[\"/\"]`. " + }, + "read_quality_score_base": { + "type": "integer", + "description": "number to be subtracted from the ASCII code to get Phred quality score", + "help_text": "Type: `integer`, multiple: `False`, example: `33`. " + } + } }, - - { - "$ref": "#/definitions/read clipping" + "read clipping": { + "title": "Read Clipping", + "type": "object", + "description": "No description", + "properties": { + "clip_adapter_type": { + "type": "string", + "description": "adapter clipping type\n\n- Hamming ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Hamming\"`. " + }, + "clip3p_nbases": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "number(s) of bases to clip from 3p of each mate", + "help_text": "Type: `integer`, multiple: `True`, example: `[0]`. " + }, + "clip3p_adapter_seq": { + "type": "array", + "items": { + "type": "string" + }, + "description": "adapter sequences to clip from 3p of each mate", + "help_text": "Type: `string`, multiple: `True`. " + }, + "clip3p_adapter_mm_p": { + "type": "array", + "items": { + "type": "number" + }, + "description": "max proportion of mismatches for 3p adapter clipping for each mate", + "help_text": "Type: `double`, multiple: `True`, example: `[0.1]`. " + }, + "clip3p_after_adapter_nbases": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "number of bases to clip from 3p of each mate after the adapter clipping", + "help_text": "Type: `integer`, multiple: `True`, example: `[0]`. " + }, + "clip5p_nbases": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "number(s) of bases to clip from 5p of each mate", + "help_text": "Type: `integer`, multiple: `True`, example: `[0]`. " + } + } }, - - { - "$ref": "#/definitions/limits" + "limits": { + "title": "Limits", + "type": "object", + "description": "No description", + "properties": { + "limit_genome_generate_ram": { + "type": "string", + "description": "maximum available RAM (bytes) for genome generation", + "help_text": "Type: `long`, multiple: `False`, example: `31000000000`. " + }, + "limit_io_buffer_size": { + "type": "array", + "items": { + "type": "string" + }, + "description": "max available buffers size (bytes) for input/output, per thread", + "help_text": "Type: `long`, multiple: `True`, example: `[30000000;50000000]`. " + }, + "limit_out_sam_one_read_bytes": { + "type": "string", + "description": "max size of the SAM record (bytes) for one read", + "help_text": "Type: `long`, multiple: `False`, example: `100000`. " + }, + "limit_out_sj_one_read": { + "type": "integer", + "description": "max number of junctions for one read (including all multi-mappers)", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "limit_out_sj_collapsed": { + "type": "integer", + "description": "max number of collapsed junctions", + "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. " + }, + "limit_bam_sort_ram": { + "type": "string", + "description": "maximum available RAM (bytes) for sorting BAM", + "help_text": "Type: `long`, multiple: `False`, example: `0`. " + }, + "limit_sjdb_insert_nsj": { + "type": "integer", + "description": "maximum number of junctions to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run", + "help_text": "Type: `integer`, multiple: `False`, example: `1000000`. " + }, + "limit_nreads_soft": { + "type": "integer", + "description": "soft limit on the number of reads", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + } + } }, - - { - "$ref": "#/definitions/output: general" + "output: general": { + "title": "Output: general", + "type": "object", + "description": "No description", + "properties": { + "out_tmp_keep": { + "type": "string", + "description": "whether to keep the temporary files after STAR runs is finished\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_std": { + "type": "string", + "description": "which output will be directed to stdout (standard out)\n\n- Log ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Log\"`. " + }, + "out_reads_unmapped": { + "type": "string", + "description": "output of unmapped and partially mapped (i.e", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_qs_conversion_add": { + "type": "integer", + "description": "add this number to the quality score (e.g", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "out_multimapper_order": { + "type": "string", + "description": "order of multimapping alignments in the output files\n\n- Old_2.4 ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Old_2.4\"`. " + } + } }, - - { - "$ref": "#/definitions/output: sam and bam" + "output: sam and bam": { + "title": "Output: SAM and BAM", + "type": "object", + "description": "No description", + "properties": { + "out_sam_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of SAM/BAM output\n\n1st word:\n- BAM ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"SAM\"]`. " + }, + "out_sam_mode": { + "type": "string", + "description": "mode of SAM output\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Full\"`. " + }, + "out_sam_strand_field": { + "type": "string", + "description": "Cufflinks-like strand field flag\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_sam_attributes": { + "type": "array", + "items": { + "type": "string" + }, + "description": "a string of desired SAM attributes, in the order desired for the output SAM", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Standard\"]`. " + }, + "out_sam_attr_ih_start": { + "type": "integer", + "description": "start value for the IH attribute", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "out_sam_unmapped": { + "type": "array", + "items": { + "type": "string" + }, + "description": "output of unmapped reads in the SAM format\n\n1st word:\n- None ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_sam_order": { + "type": "string", + "description": "type of sorting for the SAM output\n\nPaired: one mate after the other for all paired alignments\nPairedKeepInputOrder: one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files", + "help_text": "Type: `string`, multiple: `False`, example: `\"Paired\"`. " + }, + "out_sam_primary_flag": { + "type": "string", + "description": "which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG\n\n- OneBestScore ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"OneBestScore\"`. " + }, + "out_sam_read_id": { + "type": "string", + "description": "read ID record type\n\n- Standard ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Standard\"`. " + }, + "out_sam_mapq_unique": { + "type": "integer", + "description": "0 to 255: the MAPQ value for unique mappers", + "help_text": "Type: `integer`, multiple: `False`, example: `255`. " + }, + "out_sam_flag_or": { + "type": "integer", + "description": "0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "out_sam_flag_and": { + "type": "integer", + "description": "0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e", + "help_text": "Type: `integer`, multiple: `False`, example: `65535`. " + }, + "out_sam_attr_rg_line": { + "type": "array", + "items": { + "type": "string" + }, + "description": "SAM/BAM read group line", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_sam_header_hd": { + "type": "array", + "items": { + "type": "string" + }, + "description": "@HD (header) line of the SAM header", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_sam_header_pg": { + "type": "array", + "items": { + "type": "string" + }, + "description": "extra @PG (software) line of the SAM header (in addition to STAR)", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_sam_header_comment_file": { + "type": "string", + "description": "path to the file with @CO (comment) lines of the SAM header", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_sam_filter": { + "type": "array", + "items": { + "type": "string" + }, + "description": "filter the output into main SAM/BAM files\n\n- KeepOnlyAddedReferences ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_sam_mult_nmax": { + "type": "integer", + "description": "max number of multiple alignments for a read that will be output to the SAM/BAM files", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "out_sam_tlen": { + "type": "integer", + "description": "calculation method for the TLEN field in the SAM/BAM files\n\n- 1 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "out_bam_compression": { + "type": "integer", + "description": "-1 to 10 BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "out_bam_sorting_thread_n": { + "type": "integer", + "description": ">=0: number of threads for BAM sorting", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "out_bam_sorting_bins_n": { + "type": "integer", + "description": ">0: number of genome bins for coordinate-sorting", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + } + } }, - - { - "$ref": "#/definitions/bam processing" + "bam processing": { + "title": "BAM processing", + "type": "object", + "description": "No description", + "properties": { + "bam_remove_duplicates_type": { + "type": "string", + "description": "mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only\n\n- - ..", + "help_text": "Type: `string`, multiple: `False`. " + }, + "bam_remove_duplicates_mate2bases_n": { + "type": "integer", + "description": "number of bases from the 5' of mate 2 to use in collapsing (e.g", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + } + } }, - - { - "$ref": "#/definitions/output wiggle" + "output wiggle": { + "title": "Output Wiggle", + "type": "object", + "description": "No description", + "properties": { + "out_wig_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of signal output, e.g", + "help_text": "Type: `string`, multiple: `True`. " + }, + "out_wig_strand": { + "type": "string", + "description": "strandedness of wiggle/bedGraph output\n\n- Stranded ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Stranded\"`. " + }, + "out_wig_references_prefix": { + "type": "string", + "description": "prefix matching reference names to include in the output wiggle file, e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_wig_norm": { + "type": "string", + "description": "type of normalization for the signal\n\n- RPM ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"RPM\"`. " + } + } }, - - { - "$ref": "#/definitions/output filtering" + "output filtering": { + "title": "Output Filtering", + "type": "object", + "description": "No description", + "properties": { + "out_filter_type": { + "type": "string", + "description": "type of filtering\n\n- Normal ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Normal\"`. " + }, + "out_filter_multimap_score_range": { + "type": "integer", + "description": "the score range below the maximum score for multimapping alignments", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "out_filter_multimap_nmax": { + "type": "integer", + "description": "maximum number of loci the read is allowed to map to", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "out_filter_mismatch_nmax": { + "type": "integer", + "description": "alignment will be output only if it has no more mismatches than this value.", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "out_filter_mismatch_nover_lmax": { + "type": "number", + "description": "alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value.", + "help_text": "Type: `double`, multiple: `False`, example: `0.3`. " + }, + "out_filter_mismatch_nover_read_lmax": { + "type": "number", + "description": "alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value.", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + }, + "out_filter_score_min": { + "type": "integer", + "description": "alignment will be output only if its score is higher than or equal to this value.", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "out_filter_score_min_over_lread": { + "type": "number", + "description": "same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads)", + "help_text": "Type: `double`, multiple: `False`, example: `0.66`. " + }, + "out_filter_match_nmin": { + "type": "integer", + "description": "alignment will be output only if the number of matched bases is higher than or equal to this value.", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "out_filter_match_nmin_over_lread": { + "type": "number", + "description": "sam as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads).", + "help_text": "Type: `double`, multiple: `False`, example: `0.66`. " + }, + "out_filter_intron_motifs": { + "type": "string", + "description": "filter alignment using their motifs\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`. " + }, + "out_filter_intron_strands": { + "type": "string", + "description": "filter alignments\n\n- RemoveInconsistentStrands ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"RemoveInconsistentStrands\"`. " + } + } }, - - { - "$ref": "#/definitions/output splice junctions (sj.out.tab)" + "output splice junctions (sj.out.tab)": { + "title": "Output splice junctions (SJ.out.tab)", + "type": "object", + "description": "No description", + "properties": { + "out_sj_type": { + "type": "string", + "description": "type of splice junction output\n\n- Standard ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Standard\"`. " + } + } }, - - { - "$ref": "#/definitions/output filtering: splice junctions" + "output filtering: splice junctions": { + "title": "Output Filtering: Splice Junctions", + "type": "object", + "description": "No description", + "properties": { + "out_sj_filter_reads": { + "type": "string", + "description": "which reads to consider for collapsed splice junctions output\n\n- All ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"All\"`. " + }, + "out_sj_filter_overhang_min": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", + "help_text": "Type: `integer`, multiple: `True`, example: `[30;12;12;12]`. " + }, + "out_sj_filter_count_unique_min": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", + "help_text": "Type: `integer`, multiple: `True`, example: `[3;1;1;1]`. " + }, + "out_sj_filter_count_total_min": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif", + "help_text": "Type: `integer`, multiple: `True`, example: `[3;1;1;1]`. " + }, + "out_sj_filter_dist_to_other_sj_min": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "minimum allowed distance to other junctions' donor/acceptor\n\ndoes not apply to annotated junctions", + "help_text": "Type: `integer`, multiple: `True`, example: `[10;0;5;10]`. " + }, + "out_sj_filter_intron_max_vs_read_n": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "maximum gap allowed for junctions supported by 1,2,3,,,N reads\n\ni.e", + "help_text": "Type: `integer`, multiple: `True`, example: `[50000;100000;200000]`. " + } + } }, - - { - "$ref": "#/definitions/scoring" + "scoring": { + "title": "Scoring", + "type": "object", + "description": "No description", + "properties": { + "score_gap": { + "type": "integer", + "description": "splice junction penalty (independent on intron motif)", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "score_gap_noncan": { + "type": "integer", + "description": "non-canonical junction penalty (in addition to scoreGap)", + "help_text": "Type: `integer`, multiple: `False`, example: `-8`. " + }, + "score_gap_gcag": { + "type": "integer", + "description": "GC/AG and CT/GC junction penalty (in addition to scoreGap)", + "help_text": "Type: `integer`, multiple: `False`, example: `-4`. " + }, + "score_gap_atac": { + "type": "integer", + "description": "AT/AC and GT/AT junction penalty (in addition to scoreGap)", + "help_text": "Type: `integer`, multiple: `False`, example: `-8`. " + }, + "score_genomic_length_log2scale": { + "type": "integer", + "description": "extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "score_del_open": { + "type": "integer", + "description": "deletion open penalty", + "help_text": "Type: `integer`, multiple: `False`, example: `-2`. " + }, + "score_del_base": { + "type": "integer", + "description": "deletion extension penalty per base (in addition to scoreDelOpen)", + "help_text": "Type: `integer`, multiple: `False`, example: `-2`. " + }, + "score_ins_open": { + "type": "integer", + "description": "insertion open penalty", + "help_text": "Type: `integer`, multiple: `False`, example: `-2`. " + }, + "score_ins_base": { + "type": "integer", + "description": "insertion extension penalty per base (in addition to scoreInsOpen)", + "help_text": "Type: `integer`, multiple: `False`, example: `-2`. " + }, + "score_stitch_sj_shift": { + "type": "integer", + "description": "maximum score reduction while searching for SJ boundaries in the stitching step", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + } + } }, - - { - "$ref": "#/definitions/alignments and seeding" + "alignments and seeding": { + "title": "Alignments and Seeding", + "type": "object", + "description": "No description", + "properties": { + "seed_search_start_lmax": { + "type": "integer", + "description": "defines the search start point through the read - the read is split into pieces no longer than this value", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + }, + "seed_search_start_lmax_over_lread": { + "type": "number", + "description": "seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads)", + "help_text": "Type: `double`, multiple: `False`, example: `1.0`. " + }, + "seed_search_lmax": { + "type": "integer", + "description": "defines the maximum length of the seeds, if =0 seed length is not limited", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "seed_multimap_nmax": { + "type": "integer", + "description": "only pieces that map fewer than this value are utilized in the stitching procedure", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "seed_per_read_nmax": { + "type": "integer", + "description": "max number of seeds per read", + "help_text": "Type: `integer`, multiple: `False`, example: `1000`. " + }, + "seed_per_window_nmax": { + "type": "integer", + "description": "max number of seeds per window", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + }, + "seed_none_loci_per_window": { + "type": "integer", + "description": "max number of one seed loci per window", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "seed_split_min": { + "type": "integer", + "description": "min length of the seed sequences split by Ns or mate gap", + "help_text": "Type: `integer`, multiple: `False`, example: `12`. " + }, + "seed_map_min": { + "type": "integer", + "description": "min length of seeds to be mapped", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "align_intron_min": { + "type": "integer", + "description": "minimum intron size, genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion", + "help_text": "Type: `integer`, multiple: `False`, example: `21`. " + }, + "align_intron_max": { + "type": "integer", + "description": "maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "align_mates_gap_max": { + "type": "integer", + "description": "maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "align_sj_overhang_min": { + "type": "integer", + "description": "minimum overhang (i.e", + "help_text": "Type: `integer`, multiple: `False`, example: `5`. " + }, + "align_sj_stitch_mismatch_nmax": { + "type": "array", + "items": { + "type": "integer" + }, + "description": "maximum number of mismatches for stitching of the splice junctions (-1: no limit).\n\n(1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif.", + "help_text": "Type: `integer`, multiple: `True`, example: `[0;-1;0;0]`. " + }, + "align_sjdb_overhang_min": { + "type": "integer", + "description": "minimum overhang (i.e", + "help_text": "Type: `integer`, multiple: `False`, example: `3`. " + }, + "align_spliced_mate_map_lmin": { + "type": "integer", + "description": "minimum mapped length for a read mate that is spliced", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "align_spliced_mate_map_lmin_over_lmate": { + "type": "number", + "description": "alignSplicedMateMapLmin normalized to mate length", + "help_text": "Type: `double`, multiple: `False`, example: `0.66`. " + }, + "align_windows_per_read_nmax": { + "type": "integer", + "description": "max number of windows per read", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "align_transcripts_per_window_nmax": { + "type": "integer", + "description": "max number of transcripts per window", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "align_transcripts_per_read_nmax": { + "type": "integer", + "description": "max number of different alignments per read to consider", + "help_text": "Type: `integer`, multiple: `False`, example: `10000`. " + }, + "align_ends_type": { + "type": "string", + "description": "type of read ends alignment\n\n- Local ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Local\"`. " + }, + "align_ends_protrude": { + "type": "string", + "description": "allow protrusion of alignment ends, i.e", + "help_text": "Type: `string`, multiple: `False`, example: `\"0 ConcordantPair\"`. " + }, + "align_soft_clip_at_reference_ends": { + "type": "string", + "description": "allow the soft-clipping of the alignments past the end of the chromosomes\n\n- Yes ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Yes\"`. " + }, + "align_insertion_flush": { + "type": "string", + "description": "how to flush ambiguous insertion positions\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/paired-end reads" + "paired-end reads": { + "title": "Paired-End reads", + "type": "object", + "description": "No description", + "properties": { + "pe_overlap_nbases_min": { + "type": "integer", + "description": "minimum number of overlapping bases to trigger mates merging and realignment", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "pe_overlap_mm_p": { + "type": "number", + "description": "maximum proportion of mismatched bases in the overlap area", + "help_text": "Type: `double`, multiple: `False`, example: `0.01`. " + } + } }, - - { - "$ref": "#/definitions/windows, anchors, binning" + "windows, anchors, binning": { + "title": "Windows, Anchors, Binning", + "type": "object", + "description": "No description", + "properties": { + "win_anchor_multimap_nmax": { + "type": "integer", + "description": "max number of loci anchors are allowed to map to", + "help_text": "Type: `integer`, multiple: `False`, example: `50`. " + }, + "win_bin_nbits": { + "type": "integer", + "description": "=log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins.", + "help_text": "Type: `integer`, multiple: `False`, example: `16`. " + }, + "win_anchor_dist_nbins": { + "type": "integer", + "description": "max number of bins between two anchors that allows aggregation of anchors into one window", + "help_text": "Type: `integer`, multiple: `False`, example: `9`. " + }, + "win_flank_nbins": { + "type": "integer", + "description": "log2(winFlank), where win Flank is the size of the left and right flanking regions for each window", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "win_read_coverage_relative_min": { + "type": "number", + "description": "minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only.", + "help_text": "Type: `double`, multiple: `False`, example: `0.5`. " + }, + "win_read_coverage_bases_min": { + "type": "integer", + "description": "minimum number of bases covered by the seeds in a window , for STARlong algorithm only.", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + } + } }, - - { - "$ref": "#/definitions/chimeric alignments" + "chimeric alignments": { + "title": "Chimeric Alignments", + "type": "object", + "description": "No description", + "properties": { + "chim_out_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of chimeric output\n\n- Junctions ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Junctions\"]`. " + }, + "chim_segment_min": { + "type": "integer", + "description": "minimum length of chimeric segment length, if ==0, no chimeric output", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "chim_score_min": { + "type": "integer", + "description": "minimum total (summed) score of the chimeric segments", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "chim_score_drop_max": { + "type": "integer", + "description": "max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "chim_score_separation": { + "type": "integer", + "description": "minimum difference (separation) between the best chimeric score and the next one", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "chim_score_junction_non_gtag": { + "type": "integer", + "description": "penalty for a non-GT/AG chimeric junction", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "chim_junction_overhang_min": { + "type": "integer", + "description": "minimum overhang for a chimeric junction", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "chim_segment_read_gap_max": { + "type": "integer", + "description": "maximum gap in the read sequence between chimeric segments", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "chim_filter": { + "type": "array", + "items": { + "type": "string" + }, + "description": "different filters for chimeric alignments\n\n- None ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"banGenomicN\"]`. " + }, + "chim_main_segment_mult_nmax": { + "type": "integer", + "description": "maximum number of multi-alignments for the main chimeric segment", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "chim_multimap_nmax": { + "type": "integer", + "description": "maximum number of chimeric multi-alignments\n\n- 0 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "chim_multimap_score_range": { + "type": "integer", + "description": "the score range for multi-mapping chimeras below the best chimeric score", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "chim_nonchim_score_drop_min": { + "type": "integer", + "description": "to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "chim_out_junction_format": { + "type": "integer", + "description": "formatting type for the Chimeric.out.junction file\n\n- 0 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + } + } }, - - { - "$ref": "#/definitions/quantification of annotations" + "quantification of annotations": { + "title": "Quantification of Annotations", + "type": "object", + "description": "No description", + "properties": { + "quant_mode": { + "type": "array", + "items": { + "type": "string" + }, + "description": "types of quantification requested\n\n- - ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "quant_transcriptome_bam_compression": { + "type": "integer", + "description": "-2 to 10 transcriptome BAM compression level\n\n- -2 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "quant_transcriptome_sam_output": { + "type": "string", + "description": "alignment filtering for TranscriptomeSAM output\n\n- BanSingleEnd_BanIndels_ExtendSoftclip ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"BanSingleEnd_BanIndels_ExtendSoftclip\"`. " + } + } }, - - { - "$ref": "#/definitions/2-pass mapping" + "2-pass mapping": { + "title": "2-pass Mapping", + "type": "object", + "description": "No description", + "properties": { + "twopass_mode": { + "type": "string", + "description": "2-pass mapping mode.\n\n- None ..", + "help_text": "Type: `string`, multiple: `False`. " + }, + "twopass1reads_n": { + "type": "integer", + "description": "number of reads to process for the 1st step", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + } + } }, - - { - "$ref": "#/definitions/wasp parameters" + "wasp parameters": { + "title": "WASP parameters", + "type": "object", + "description": "No description", + "properties": { + "wasp_output_mode": { + "type": "string", + "description": "WASP allele-specific output type", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/starsolo (single cell rna-seq) parameters" + "starsolo (single cell rna-seq) parameters": { + "title": "STARsolo (single cell RNA-seq) parameters", + "type": "object", + "description": "No description", + "properties": { + "solo_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of single-cell RNA-seq\n\n- CB_UMI_Simple ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_cb_type": { + "type": "string", + "description": "cell barcode type\n\nSequence: cell barcode is a sequence (standard option)\nString: cell barcode is an arbitrary string", + "help_text": "Type: `string`, multiple: `False`, example: `\"Sequence\"`. " + }, + "solo_cb_whitelist": { + "type": "array", + "items": { + "type": "string" + }, + "description": "file(s) with whitelist(s) of cell barcodes", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_cb_start": { + "type": "integer", + "description": "cell barcode start base", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "solo_cb_len": { + "type": "integer", + "description": "cell barcode length", + "help_text": "Type: `integer`, multiple: `False`, example: `16`. " + }, + "solo_umi_start": { + "type": "integer", + "description": "UMI start base", + "help_text": "Type: `integer`, multiple: `False`, example: `17`. " + }, + "solo_umi_len": { + "type": "integer", + "description": "UMI length", + "help_text": "Type: `integer`, multiple: `False`, example: `10`. " + }, + "solo_barcode_read_length": { + "type": "integer", + "description": "length of the barcode read\n\n- 1 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "solo_barcode_mate": { + "type": "integer", + "description": "identifies which read mate contains the barcode (CB+UMI) sequence\n\n- 0 ..", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "solo_cb_position": { + "type": "array", + "items": { + "type": "string" + }, + "description": "position of Cell Barcode(s) on the barcode read.\n\nPresently only works with --solo_type CB_UMI_Complex, and barcodes are assumed to be on Read2.\nFormat for each barcode: startAnchor_startPosition_endAnchor_endPosition\nstart(end)Anchor defines the Anchor Base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end\nstart(end)Position is the 0-based position with of the CB start(end) with respect to the Anchor Base\nString for different barcodes are separated by space.\nExample: inDrop (Zilionis et al, Nat", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_umi_position": { + "type": "string", + "description": "position of the UMI on the barcode read, same as soloCBposition\n\nExample: inDrop (Zilionis et al, Nat", + "help_text": "Type: `string`, multiple: `False`. " + }, + "solo_adapter_sequence": { + "type": "string", + "description": "adapter sequence to anchor barcodes", + "help_text": "Type: `string`, multiple: `False`. " + }, + "solo_adapter_mismatches_nmax": { + "type": "integer", + "description": "maximum number of mismatches allowed in adapter sequence.", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "solo_cb_match_wl_type": { + "type": "string", + "description": "matching the Cell Barcodes to the WhiteList\n\n- Exact ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"1MM_multi\"`. " + }, + "solo_input_sam_attr_barcode_seq": { + "type": "array", + "items": { + "type": "string" + }, + "description": "when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode sequence (in proper order).\n\nFor instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_seq CR UR .\nThis parameter is required when running STARsolo with input from SAM.", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_input_sam_attr_barcode_qual": { + "type": "array", + "items": { + "type": "string" + }, + "description": "when inputting reads from a SAM file (--readsFileType SAM SE/PE), these SAM attributes mark the barcode qualities (in proper order).\n\nFor instance, for 10X CellRanger or STARsolo BAMs, use --solo_input_sam_attr_barcode_qual CY UY .\nIf this parameter is '-' (default), the quality 'H' will be assigned to all bases.", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_strand": { + "type": "string", + "description": "strandedness of the solo libraries:\n\n- Unstranded ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"Forward\"`. " + }, + "solo_features": { + "type": "array", + "items": { + "type": "string" + }, + "description": "genomic features for which the UMI counts per Cell Barcode are collected\n\n- Gene ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Gene\"]`. " + }, + "solo_multi_mappers": { + "type": "array", + "items": { + "type": "string" + }, + "description": "counting method for reads mapping to multiple genes\n\n- Unique ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Unique\"]`. " + }, + "solo_umi_dedup": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of UMI deduplication (collapsing) algorithm\n\n- 1MM_All ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"1MM_All\"]`. " + }, + "solo_umi_filtering": { + "type": "array", + "items": { + "type": "string" + }, + "description": "type of UMI filtering (for reads uniquely mapping to genes)\n\n- - ..", + "help_text": "Type: `string`, multiple: `True`. " + }, + "solo_out_file_names": { + "type": "array", + "items": { + "type": "string" + }, + "description": "file names for STARsolo output:\n\nfile_name_prefix gene_names barcode_sequences cell_feature_count_matrix", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Solo.out/\";\"features.tsv\";\"barcodes.tsv\";\"matrix.mtx\"]`. " + }, + "solo_cell_filter": { + "type": "array", + "items": { + "type": "string" + }, + "description": "cell filtering type and parameters\n\n- None ..", + "help_text": "Type: `string`, multiple: `True`, example: `[\"CellRanger2.2\";\"3000\";\"0.99\";\"10\"]`. " + }, + "solo_out_format_features_gene_field3": { + "type": "array", + "items": { + "type": "string" + }, + "description": "field 3 in the Gene features.tsv file", + "help_text": "Type: `string`, multiple: `True`, example: `[\"Gene Expression\"]`. " + }, + "solo_cell_read_stats": { + "type": "string", + "description": "Output reads statistics for each CB\n\n- Standard ..", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/run parameters" + }, + { + "$ref": "#/$defs/genome parameters" + }, + { + "$ref": "#/$defs/splice junctions database" + }, + { + "$ref": "#/$defs/variation parameters" + }, + { + "$ref": "#/$defs/read parameters" + }, + { + "$ref": "#/$defs/read clipping" + }, + { + "$ref": "#/$defs/limits" + }, + { + "$ref": "#/$defs/output: general" + }, + { + "$ref": "#/$defs/output: sam and bam" + }, + { + "$ref": "#/$defs/bam processing" + }, + { + "$ref": "#/$defs/output wiggle" + }, + { + "$ref": "#/$defs/output filtering" + }, + { + "$ref": "#/$defs/output splice junctions (sj.out.tab)" + }, + { + "$ref": "#/$defs/output filtering: splice junctions" + }, + { + "$ref": "#/$defs/scoring" + }, + { + "$ref": "#/$defs/alignments and seeding" + }, + { + "$ref": "#/$defs/paired-end reads" + }, + { + "$ref": "#/$defs/windows, anchors, binning" + }, + { + "$ref": "#/$defs/chimeric alignments" + }, + { + "$ref": "#/$defs/quantification of annotations" + }, + { + "$ref": "#/$defs/2-pass mapping" + }, + { + "$ref": "#/$defs/wasp parameters" + }, + { + "$ref": "#/$defs/starsolo (single cell rna-seq) parameters" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index c594636e..0231bd63 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Input" arguments: @@ -336,9 +331,9 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -363,6 +358,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 677ad49f..72a57b94 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -3425,9 +3417,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3443,6 +3435,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/star/star_genome_generate/nextflow_schema.json b/target/nextflow/star/star_genome_generate/nextflow_schema.json index 27f6172f..fb107044 100644 --- a/target/nextflow/star/star_genome_generate/nextflow_schema.json +++ b/target/nextflow/star/star_genome_generate/nextflow_schema.json @@ -1,245 +1,145 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "star_genome_generate", -"description": "Create index for STAR\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "genome_fasta_files": { - "type": - "string", - "description": "Type: List of `file`, required, multiple_sep: `\";\"`. Path(s) to the fasta files with the genome sequences, separated by spaces", - "help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped.\n" - - } - - - , - "sjdb_gtf_file": { - "type": - "string", - "description": "Type: `file`. Path to the GTF file with annotations", - "help_text": "Type: `file`. Path to the GTF file with annotations" - - } - - - , - "sjdb_overhang": { - "type": - "integer", - "description": "Type: `integer`, example: `100`. Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)", - "help_text": "Type: `integer`, example: `100`. Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)" - - } - - - , - "sjdb_gtf_chr_prefix": { - "type": - "string", - "description": "Type: `string`. Prefix for chromosome names in a GTF file (e", - "help_text": "Type: `string`. Prefix for chromosome names in a GTF file (e.g. \u0027chr\u0027 for using ENSMEBL annotations with UCSC genomes)" - - } - - - , - "sjdb_gtf_feature_exon": { - "type": - "string", - "description": "Type: `string`, example: `exon`. Feature type in GTF file to be used as exons for building transcripts", - "help_text": "Type: `string`, example: `exon`. Feature type in GTF file to be used as exons for building transcripts" - - } - - - , - "sjdb_gtf_tag_exon_parent_transcript": { - "type": - "string", - "description": "Type: `string`, example: `transcript_id`. GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)", - "help_text": "Type: `string`, example: `transcript_id`. GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene": { - "type": - "string", - "description": "Type: `string`, example: `gene_id`. GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)", - "help_text": "Type: `string`, example: `gene_id`. GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene_name": { - "type": - "string", - "description": "Type: List of `string`, example: `gene_name`, multiple_sep: `\";\"`. GTF attribute name for parent gene name", - "help_text": "Type: List of `string`, example: `gene_name`, multiple_sep: `\";\"`. GTF attribute name for parent gene name" - - } - - - , - "sjdb_gtf_tag_exon_parent_gene_type": { - "type": - "string", - "description": "Type: List of `string`, example: `gene_type;gene_biotype`, multiple_sep: `\";\"`. GTF attribute name for parent gene type", - "help_text": "Type: List of `string`, example: `gene_type;gene_biotype`, multiple_sep: `\";\"`. GTF attribute name for parent gene type" - - } - - - , - "limit_genome_generate_ram": { - "type": - "string", - "description": "Type: `long`, example: `31000000000`. Maximum available RAM (bytes) for genome generation", - "help_text": "Type: `long`, example: `31000000000`. Maximum available RAM (bytes) for genome generation" - - } - - - , - "genome_sa_index_nbases": { - "type": - "integer", - "description": "Type: `integer`, example: `14`. Length (bases) of the SA pre-indexing string", - "help_text": "Type: `integer`, example: `14`. Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, this parameter must be scaled down to min(14, log2(GenomeLength)/2 - 1)." - - } - - - , - "genome_chr_bin_nbits": { - "type": - "integer", - "description": "Type: `integer`, example: `18`. Defined as log2(chrBin), where chrBin is the size of the bins for genome storage", - "help_text": "Type: `integer`, example: `18`. Defined as log2(chrBin), where chrBin is the size of the bins for genome storage. Each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)])." - - } - - - , - "genome_sa_sparse_d": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Suffux array sparsity, i", - "help_text": "Type: `integer`, example: `1`. Suffux array sparsity, i.e. distance between indices. Use bigger numbers to decrease needed RAM at the cost of mapping speed reduction." - - } - - - , - "genome_suffix_length_max": { - "type": - "integer", - "description": "Type: `integer`, example: `-1`. Maximum length of the suffixes, has to be longer than read length", - "help_text": "Type: `integer`, example: `-1`. Maximum length of the suffixes, has to be longer than read length. Use -1 for infinite length." - - } - - - , - "genome_transform_type": { - "type": - "string", - "description": "Type: `string`, example: `None`. Type of genome transformation\n None ", - "help_text": "Type: `string`, example: `None`. Type of genome transformation\n None ... no transformation\n Haploid ... replace reference alleles with alternative alleles from VCF file (e.g. consensus allele)\n Diploid ... create two haplotypes for each chromosome listed in VCF file, for genotypes 1|2, assumes perfect phasing (e.g. personal genome)\n" - - } - - - , - "genome_transform_vcf": { - "type": - "string", - "description": "Type: `file`. path to VCF file for genome transformation", - "help_text": "Type: `file`. path to VCF file for genome transformation" - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "index": { - "type": - "string", - "description": "Type: `file`, required, default: `STAR_index`. STAR index directory", - "help_text": "Type: `file`, required, default: `STAR_index`. STAR index directory." - , - "default":"STAR_index" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "star_genome_generate", + "description": "Create index for STAR\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "genome_fasta_files": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Path(s) to the fasta files with the genome sequences, separated by spaces", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. " + }, + "sjdb_gtf_file": { + "type": "string", + "format": "path", + "description": "Path to the GTF file with annotations", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "sjdb_overhang": { + "type": "integer", + "description": "Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)", + "help_text": "Type: `integer`, multiple: `False`, example: `100`. " + }, + "sjdb_gtf_chr_prefix": { + "type": "string", + "description": "Prefix for chromosome names in a GTF file (e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "sjdb_gtf_feature_exon": { + "type": "string", + "description": "Feature type in GTF file to be used as exons for building transcripts", + "help_text": "Type: `string`, multiple: `False`, example: `\"exon\"`. " + }, + "sjdb_gtf_tag_exon_parent_transcript": { + "type": "string", + "description": "GTF attribute name for parent transcript ID (default \"transcript_id\" works for GTF files)", + "help_text": "Type: `string`, multiple: `False`, example: `\"transcript_id\"`. " + }, + "sjdb_gtf_tag_exon_parent_gene": { + "type": "string", + "description": "GTF attribute name for parent gene ID (default \"gene_id\" works for GTF files)", + "help_text": "Type: `string`, multiple: `False`, example: `\"gene_id\"`. " + }, + "sjdb_gtf_tag_exon_parent_gene_name": { + "type": "array", + "items": { + "type": "string" + }, + "description": "GTF attribute name for parent gene name", + "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_name\"]`. " + }, + "sjdb_gtf_tag_exon_parent_gene_type": { + "type": "array", + "items": { + "type": "string" + }, + "description": "GTF attribute name for parent gene type", + "help_text": "Type: `string`, multiple: `True`, example: `[\"gene_type\";\"gene_biotype\"]`. " + }, + "limit_genome_generate_ram": { + "type": "string", + "description": "Maximum available RAM (bytes) for genome generation", + "help_text": "Type: `long`, multiple: `False`, example: `31000000000`. " + }, + "genome_sa_index_nbases": { + "type": "integer", + "description": "Length (bases) of the SA pre-indexing string", + "help_text": "Type: `integer`, multiple: `False`, example: `14`. " + }, + "genome_chr_bin_nbits": { + "type": "integer", + "description": "Defined as log2(chrBin), where chrBin is the size of the bins for genome storage", + "help_text": "Type: `integer`, multiple: `False`, example: `18`. " + }, + "genome_sa_sparse_d": { + "type": "integer", + "description": "Suffux array sparsity, i.e", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "genome_suffix_length_max": { + "type": "integer", + "description": "Maximum length of the suffixes, has to be longer than read length", + "help_text": "Type: `integer`, multiple: `False`, example: `-1`. " + }, + "genome_transform_type": { + "type": "string", + "description": "Type of genome transformation\n None ..", + "help_text": "Type: `string`, multiple: `False`, example: `\"None\"`. " + }, + "genome_transform_vcf": { + "type": "string", + "format": "path", + "description": "path to VCF file for genome transformation", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "index": { + "type": "string", + "format": "path", + "description": "STAR index directory.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"STAR_index\"`, direction: `output`. ", + "default": "STAR_index" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 82b61277..fd72c877 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -7,13 +7,8 @@ authors: - "maintainer" info: links: - email: "nirmayi@data-intuitive.com" github: "sainirmayi" linkedin: "sai-nirmayi-yasa" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Junior Bioinformatics Researcher" argument_groups: - name: "Input" arguments: @@ -773,9 +768,9 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -800,6 +795,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index a87af2dd..cf3bfa27 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3044,17 +3044,9 @@ meta = [ ], "info" : { "links" : { - "email" : "nirmayi@data-intuitive.com", "github" : "sainirmayi", "linkedin" : "sai-nirmayi-yasa" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Junior Bioinformatics Researcher" - } - ] + } } } ], @@ -3790,9 +3782,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/trimgalore", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3808,6 +3800,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/trimgalore/nextflow_schema.json b/target/nextflow/trimgalore/nextflow_schema.json index b022cc47..94ae261d 100644 --- a/target/nextflow/trimgalore/nextflow_schema.json +++ b/target/nextflow/trimgalore/nextflow_schema.json @@ -1,711 +1,410 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "trimgalore", -"description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. \n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: List of `file`, required, example: `sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq`, multiple_sep: `\";\"`. Input files", - "help_text": "Type: List of `file`, required, example: `sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq`, multiple_sep: `\";\"`. Input files. Note that paired-end files need to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz" - - } - - -} -}, - - - "trimming options" : { - "title": "Trimming options", - "type": "object", - "description": "No description", - "properties": { - - - "quality": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. Trim low-quality ends (below the specified Phred score) from reads in addition to adapter removal", - "help_text": "Type: `integer`, example: `20`. Trim low-quality ends (below the specified Phred score) from reads in addition to adapter removal. For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract INT from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal)." - - } - - - , - "phred33": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Instructs Cutadapt to use ASCII+33 quality scores as Phred scores (Sanger/Illumina 1", - "help_text": "Type: `boolean_true`, default: `false`. Instructs Cutadapt to use ASCII+33 quality scores as Phred scores (Sanger/Illumina 1.9+ encoding) for quality trimming." - , - "default":false - } - - - , - "phred64": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Instructs Cutadapt to use ASCII+64 quality scores as Phred scores (Illumina 1", - "help_text": "Type: `boolean_true`, default: `false`. Instructs Cutadapt to use ASCII+64 quality scores as Phred scores (Illumina 1.5 encoding) for quality trimming." - , - "default":false - } - - - , - "fastqc": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Run FastQC in the default mode on the FastQ file once trimming is complete", - "help_text": "Type: `boolean_true`, default: `false`. Run FastQC in the default mode on the FastQ file once trimming is complete." - , - "default":false - } - - - , - "fastqc_args": { - "type": - "string", - "description": "Type: `string`, example: `--nogroup --noextract`. Passes extra arguments (excluding files) to FastQC", - "help_text": "Type: `string`, example: `--nogroup --noextract`. Passes extra arguments (excluding files) to FastQC. If more than one argument is to be passed to FastQC they must be in the form \"arg1 arg2 ...\". Passing extra arguments will automatically invoke FastQC, so --fastqc does not have to be specified separately." - - } - - - , - "fastqc_contaminants": { - "type": - "string", - "description": "Type: `file`, example: `contaminants.txt`. Specifies a non-default file which contains the list of contaminants for FastQC to screen overrepresented sequences against", - "help_text": "Type: `file`, example: `contaminants.txt`. Specifies a non-default file which contains the list of contaminants for FastQC to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored." - - } - - - , - "fastqc_adapters": { - "type": - "string", - "description": "Type: `file`, example: `adapters.txt`. Specifies a non-default file which contains the list of adapter sequences which which FasstQC will explicity search against the library", - "help_text": "Type: `file`, example: `adapters.txt`. Specifies a non-default file which contains the list of adapter sequences which which FasstQC will explicity search against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored." - - } - - - , - "fastqc_limits": { - "type": - "string", - "description": "Type: `file`, example: `limits.txt`. Specifies a non-default file which contains a set of criteria which FastQC will use to determine the warn/error limits for the various modules", - "help_text": "Type: `file`, example: `limits.txt`. Specifies a non-default file which contains a set of criteria which FastQC will use to determine the warn/error limits for the various modules. This file can also be used to selectively remove some modules from the output all together. The format needs to mirror the default limits.txt file found in the Configuration folder." - - } - - - , - "adapter": { - "type": - "string", - "description": "Type: `string`, example: `AGCTCCCG`. Adapter sequence to be trimmed", - "help_text": "Type: `string`, example: `AGCTCCCG`. Adapter sequence to be trimmed. If not specified explicitly, Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used. A single base may also be given as e.g. -a A{10}, to be expanded to -a AAAAAAAAAA. \nAt a special request, multiple adapters can also be specified like so: \n -a \" AGCTCCCG -a TTTCATTATAT -a TTTATTCGGATTTAT\" -a2 \" AGCTAGCG -a TCTCTTATAT -a TTTCGGATTTAT\", \nor so:\n -a \"file:../multiple_adapters.fa\" -a2 \"file:../different_adapters.fa\"\nPotentially in conjucntion with the parameter \"-n 3\" to trim all adapters. \n" - - } - - - , - "adapter2": { - "type": - "string", - "description": "Type: `string`, example: `AGCTCCCG`. Optional adapter sequence to be trimmed off read 2 of paired-end files", - "help_text": "Type: `string`, example: `AGCTCCCG`. Optional adapter sequence to be trimmed off read 2 of paired-end files. This option requires \u0027--paired\u0027 to be specified as well. If the libraries to be trimmed are smallRNA then a2 will be set to the Illumina small RNA 5\u0027 adapter automatically (GATCGTCGGACT). A single base may also be given as e.g. -a2 A{10}, to be expanded to -a2 AAAAAAAAAA." - - } - - - , - "illumina": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter \u0027AGATCGGAAGAGC\u0027 instead of the default auto-detection of adapter sequence", - "help_text": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter \u0027AGATCGGAAGAGC\u0027 instead of the default auto-detection of adapter sequence." - , - "default":false - } - - - , - "stranded_illumina": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 13bp of the Illumina stranded mRNA or Total RNA adapter \u0027ACTGTCTCTTATA\u0027 instead of the default auto-detection of adapter sequence", - "help_text": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 13bp of the Illumina stranded mRNA or Total RNA adapter \u0027ACTGTCTCTTATA\u0027 instead of the default auto-detection of adapter sequence." - , - "default":false - } - - - , - "nextera": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 12bp of the Nextera adapter \u0027CTGTCTCTTATA\u0027 instead of the default auto-detection of adapter sequence", - "help_text": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 12bp of the Nextera adapter \u0027CTGTCTCTTATA\u0027 instead of the default auto-detection of adapter sequence." - , - "default":false - } - - - , - "small_rna": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3\u0027 Adapter \u0027TGGAATTCTCGG\u0027 instead of the default auto-detection of adapter sequence", - "help_text": "Type: `boolean_true`, default: `false`. Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3\u0027 Adapter \u0027TGGAATTCTCGG\u0027 instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then a automatically (GATCGTCGGACT) unless -a 2 had been defined explicitly." - , - "default":false - } - - - , - "consider_already_trimmed": { - "type": - "integer", - "description": "Type: `integer`. During adapter auto-detection, the limit set by this argument allows the user to set a threshold up to which the file is considered already adapter-trimmed", - "help_text": "Type: `integer`. During adapter auto-detection, the limit set by this argument allows the user to set a threshold up to which the file is considered already adapter-trimmed. If no adapter sequence exceeds this threshold, no additional adapter trimming will be performed (technically, the adapter is set to \u0027-a X\u0027). Quality trimming is still performed as usual." - - } - - - , - "max_length": { - "type": - "integer", - "description": "Type: `integer`. Discard reads that are longer than the specified value after trimming", - "help_text": "Type: `integer`. Discard reads that are longer than the specified value after trimming. This is only advised for smallRNA sequencing to remove non-small RNA sequences." - - } - - - , - "stringency": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. Overlap with adapter sequence required to trim a sequence", - "help_text": "Type: `integer`, example: `1`. Overlap with adapter sequence required to trim a sequence. Defaults to a very stringent setting of 1, i.e. even a single bp of overlapping sequence will be trimmed off from the 3\u0027 end of any read." - - } - - - , - "error_rate": { - "type": - "number", - "description": "Type: `double`, example: `0.1`. Maximum allowed error rate (no", - "help_text": "Type: `double`, example: `0.1`. Maximum allowed error rate (no. of errors divided by the length of the matching region)" - - } - - - , - "gzip": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Compress the output file with GZIP", - "help_text": "Type: `boolean_true`, default: `false`. Compress the output file with GZIP. If the input files are GZIP-compressed the output files will automatically be GZIP compressed as well. As of v0.2.8 the compression will take place on the fly." - , - "default":false - } - - - , - "dont_gzip": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Output files won\u0027t be compressed with GZIP", - "help_text": "Type: `boolean_true`, default: `false`. Output files won\u0027t be compressed with GZIP. This option overrides --gzip." - , - "default":false - } - - - , - "length": { - "type": - "integer", - "description": "Type: `integer`, example: `20`. Discard reads that became shorter than the specified length because of either quality or adapter trimming", - "help_text": "Type: `integer`, example: `20`. Discard reads that became shorter than the specified length because of either quality or adapter trimming. A value of \u00270\u0027 effectively disables this behaviour. For paired-end files, both reads of a read-pair need to be longer than the specified length to be printed out to validated paired-end files. If only one read became too short there is the possibility of keeping such unpaired single-end reads using the --retain_unpaired option." - - } - - - , - "max_n": { - "type": - "integer", - "description": "Type: `integer`. The total number of Ns a read may contain before it will be removed altogether", - "help_text": "Type: `integer`. The total number of Ns a read may contain before it will be removed altogether.In a paired-end setting, either read exceeding this limit will result in the entire pair being removed from the trimmed output files. If COUNT is a number between 0 and 1, it is interpreted as a fraction of the read length." - - } - - - , - "trim_n": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Removes Ns from either side of the read", - "help_text": "Type: `boolean_true`, default: `false`. Removes Ns from either side of the read. This option does currently not work in RRBS mode." - , - "default":false - } - - - , - "no_report_file": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If specified no report file will be generated", - "help_text": "Type: `boolean_true`, default: `false`. If specified no report file will be generated." - , - "default":false - } - - - , - "suppress_warn": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If specified any output to STDOUT or STDERR will be suppressed", - "help_text": "Type: `boolean_true`, default: `false`. If specified any output to STDOUT or STDERR will be suppressed." - , - "default":false - } - - - , - "clip_R1": { - "type": - "integer", - "description": "Type: `integer`. Instructs TrimGalore to remove given number of bp from the 5\u0027 end of read 1 (or single-end reads)", - "help_text": "Type: `integer`. Instructs TrimGalore to remove given number of bp from the 5\u0027 end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5\u0027 end." - - } - - - , - "clip_R2": { - "type": - "integer", - "description": "Type: `integer`. Instructs TrimGalore to remove given number bp from the 5\u0027 end of read 2 (paired-end reads only)", - "help_text": "Type: `integer`. Instructs TrimGalore to remove given number bp from the 5\u0027 end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5\u0027 end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation." - - } - - - , - "three_prime_clip_R1": { - "type": - "integer", - "description": "Type: `integer`. Instructs Trim Galore to remove spacified number of bp from the 3\u0027 end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed", - "help_text": "Type: `integer`. Instructs Trim Galore to remove spacified number of bp from the 3\u0027 end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some bias from the 3\u0027 end that is not directly related to adapter sequence or basecall quality." - - } - - - , - "three_prime_clip_R2": { - "type": - "integer", - "description": "Type: `integer`. Instructs Trim Galore to remove \u003cint\u003e bp from the 3\u0027 end of read 2 AFTER adapter/quality trimming has been performed", - "help_text": "Type: `integer`. Instructs Trim Galore to remove \u003cint\u003e bp from the 3\u0027 end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3\u0027 end that is not directly related to adapter sequence or basecall quality." - - } - - - , - "nextseq": { - "type": - "integer", - "description": "Type: `integer`. This enables the option \u0027--nextseq-trim=3\u0027CUTOFF\u0027 within Cutadapt, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored", - "help_text": "Type: `integer`. This enables the option \u0027--nextseq-trim=3\u0027CUTOFF\u0027 within Cutadapt, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases. This is mutually exlusive with \u0027-q INT\u0027." - - } - - - , - "basename": { - "type": - "string", - "description": "Type: `string`. Use specified name (PREFERRED_NAME) as the basename for output files, instead of deriving the filenames from the input files", - "help_text": "Type: `string`. Use specified name (PREFERRED_NAME) as the basename for output files, instead of deriving the filenames from the input files. Single-end data would be called PREFERRED_NAME_trimmed.fq(.gz), or PREFERRED_NAME_val_1.fq(.gz) and PREFERRED_NAME_val_2.fq(.gz) for paired-end data. --basename only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - - } - - -} -}, - - - "specific trimming options without adapter/quality trimming" : { - "title": "Specific trimming options without adapter/quality trimming", - "type": "object", - "description": "No description", - "properties": { - - - "hardtrim5": { - "type": - "integer", - "description": "Type: `integer`. Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to \u003cint\u003e bp at the 5\u0027-end", - "help_text": "Type: `integer`. Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to \u003cint\u003e bp at the 5\u0027-end. Once hard-trimming of files is complete, Trim Galore will exit. Hard-trimmed output files will end in .\u003cint\u003e_5prime.fq(.gz)." - - } - - - , - "hardtrim3": { - "type": - "integer", - "description": "Type: `integer`. Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to \u003cint\u003e bp at the 3\u0027-end", - "help_text": "Type: `integer`. Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to \u003cint\u003e bp at the 3\u0027-end. Once hard-trimming of files is complete, Trim Galore will exit. Hard-trimmed output files will end in .\u003cint\u003e_3prime.fq(.gz)." - - } - - - , - "clock": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock", - "help_text": "Type: `boolean_true`, default: `false`. In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock." - , - "default":false - } - - - , - "polyA": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences", - "help_text": "Type: `boolean_true`, default: `false`. This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences. When --polyA is selected, Trim Galore attempts to identify from the first supplied sample whether sequences contain more often a stretch of either \u0027AAAAAAAAAA\u0027 or \u0027TTTTTTTTTT\u0027. This determines if Read 1 of a paired-end end file, or single-end files, are trimmed for PolyA or PolyT. In case of paired-end sequencing, Read2 is trimmed for the complementary base from the start of the reads. The auto-detection uses a default of A{20} for Read1 (3\u0027-end trimming) and T{150} for Read2 (5\u0027-end trimming). These values may be changed manually using the options -a and -a2. In addition to trimming the sequences, white spaces are replaced with _ and it records in the read ID how many bases were trimmed so it can later be used to identify PolyA trimmed sequences. This is currently done by writing tags to both the start (\"32:A:\") and end (\"_PolyA:32\") of the reads. The poly-A trimming mode expects that sequences were both adapter and quality before looking for Poly-A tails, and it is the user\u0027s responsibility to carry out an initial round of trimming." - , - "default":false - } - - - , - "implicon": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads", - "help_text": "Type: `boolean_true`, default: `false`. This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads. Following this, Trim Galore will exit. In it\u0027s current implementation, the UMI carrying reads come in the following format\n Read 1 5\u0027 FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 3\u0027\n Read 2 3\u0027 UUUUUUUUFFFFFFFFFFFFFFFFFFFFFFFFFFFF 5\u0027\nWhere UUUUUUUU is a random 8-mer unique molecular identifier (UMI) and FFFFFFF... is the actual fragment to be sequenced. The UMI of Read 2 (R2) is written into the read ID of both reads and removed from the actual sequence.\n" - , - "default":false - } - - -} -}, - - - "rrbs-specific options" : { - "title": "RRBS-specific options", - "type": "object", - "description": "No description", - "properties": { - - - "rrbs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Specifies that the input file was an MspI digested RRBS sample (recognition site is CCGG)", - "help_text": "Type: `boolean_true`, default: `false`. Specifies that the input file was an MspI digested RRBS sample (recognition site is CCGG). Single-end or Read 1 sequences (paired-end) which were adapter-trimmed will have a further 2 bp removed from their 3\u0027 end. Sequences which were merely trimmed because of poor quality will not be shortened further. Read 2 of paired-end libraries will in addition have the first 2 bp removed from the 5\u0027 end (by setting \u0027--clip_r2 2\u0027). This is to avoid using artificial methylation calls from the filled-in cytosine positions close to the 3\u0027 MspI site in sequenced fragments. This option is not recommended for users of the Tecan Ovation RRBS Methyl-Seq with TrueMethyl oxBS 1-16 kit (see below)." - , - "default":false - } - - - , - "non_directional": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for \u0027CAA\u0027 or \u0027CGA\u0027 at the start of the read and, if found, removes the first two basepairs", - "help_text": "Type: `boolean_true`, default: `false`. Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for \u0027CAA\u0027 or \u0027CGA\u0027 at the start of the read and, if found, removes the first two basepairs. Like with the option \u0027--rrbs\u0027 this avoids using cytosine positions that were filled-in during the end-repair step. \u0027--non_directional\u0027 requires \u0027--rrbs\u0027 to be specified as well. Note that this option does not set \u0027--clip_r2 2\u0027 in paired-end mode." - , - "default":false - } - - - , - "keep": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Keep the quality trimmed intermediate file", - "help_text": "Type: `boolean_true`, default: `false`. Keep the quality trimmed intermediate file." - , - "default":false - } - - -} -}, - - - "paired-end specific options" : { - "title": "Paired-end specific options", - "type": "object", - "description": "No description", - "properties": { - - - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. This option performs length trimming of quality/adapter/RRBS trimmed reads for paired-end files", - "help_text": "Type: `boolean_true`, default: `false`. This option performs length trimming of quality/adapter/RRBS trimmed reads for paired-end files. To pass the validation test, both sequences of a sequence pair are required to have a certain minimum length which is governed by the option --length (see above). If only one read passes this length threshold the other read can be rescued (see option --retain_unpaired). Using this option lets you discard too short read pairs without disturbing the sequence-by-sequence order of FastQ files which is required by many aligners. Trim Galore expects paired-end files to be supplied in a pairwise fashion, e.g. file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz ... ." - , - "default":false - } - - - , - "retain_unpaired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. If only one of the two paired-end reads became too short, the longer read will be written to either \u0027", - "help_text": "Type: `boolean_true`, default: `false`. If only one of the two paired-end reads became too short, the longer read will be written to either \u0027.unpaired_1.fq\u0027 or \u0027.unpaired_2.fq\u0027 output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2." - , - "default":false - } - - - , - "length_1": { - "type": - "integer", - "description": "Type: `integer`, example: `35`. Unpaired single-end read length cutoff needed for read 1 to be written to \u0027", - "help_text": "Type: `integer`, example: `35`. Unpaired single-end read length cutoff needed for read 1 to be written to \u0027.unpaired_1.fq\u0027 output file. These reads may be mapped in single-end mode." - - } - - - , - "length_2": { - "type": - "integer", - "description": "Type: `integer`, example: `35`. Unpaired single-end read length cutoff needed for read 2 to be written to \u0027", - "help_text": "Type: `integer`, example: `35`. Unpaired single-end read length cutoff needed for read 2 to be written to \u0027.unpaired_2.fq\u0027 output file. These reads may be mapped in single-end mode." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output_dir": { - "type": - "string", - "description": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory", - "help_text": "Type: `file`, required, default: `trimmed_output`. If specified all output will be written to this directory instead of the current directory." - , - "default":"trimmed_output" - } - - - , - "trimmed_r1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_r1.fastq`, example: `read_1.fastq`. Output file for read 1", - "help_text": "Type: `file`, default: `$id.$key.trimmed_r1.fastq`, example: `read_1.fastq`. Output file for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_r1.fastq" - } - - - , - "trimmed_r2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_r2.fastq`, example: `read_2.fastq`. Output file for read 2", - "help_text": "Type: `file`, default: `$id.$key.trimmed_r2.fastq`, example: `read_2.fastq`. Output file for read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_r2.fastq" - } - - - , - "trimming_report_r1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimming_report_r1.txt`, example: `read_1.trimming_report.txt`. Trimming report for read 1", - "help_text": "Type: `file`, default: `$id.$key.trimming_report_r1.txt`, example: `read_1.trimming_report.txt`. Trimming report for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimming_report_r1.txt" - } - - - , - "trimming_report_r2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimming_report_r2.txt`, example: `read_2.trimming_report.txt`. Trimming report for read 1", - "help_text": "Type: `file`, default: `$id.$key.trimming_report_r2.txt`, example: `read_2.trimming_report.txt`. Trimming report for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimming_report_r2.txt" - } - - - , - "trimmed_fastqc_html_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_1.html`, example: `read_1.fastqc.html`. FastQC report for trimmed (single-end) reads (or read 1 for paired-end)", - "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_1.html`, example: `read_1.fastqc.html`. FastQC report for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_fastqc_html_1.html" - } - - - , - "trimmed_fastqc_html_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_2.html`, example: `read_2.fastqc.html`. FastQC report for trimmed reads (read2 for paired-end)", - "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_html_2.html`, example: `read_2.fastqc.html`. FastQC report for trimmed reads (read2 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_fastqc_html_2.html" - } - - - , - "trimmed_fastqc_zip_1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_1.zip`, example: `read_1.fastqc.zip`. FastQC results for trimmed (single-end) reads (or read 1 for paired-end)", - "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_1.zip`, example: `read_1.fastqc.zip`. FastQC results for trimmed (single-end) reads (or read 1 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_fastqc_zip_1.zip" - } - - - , - "trimmed_fastqc_zip_2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_2.zip`, example: `read_2.fastqc.zip`. FastQC results for trimmed reads (read2 for paired-end)", - "help_text": "Type: `file`, default: `$id.$key.trimmed_fastqc_zip_2.zip`, example: `read_2.fastqc.zip`. FastQC results for trimmed reads (read2 for paired-end). Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.trimmed_fastqc_zip_2.zip" - } - - - , - "unpaired_r1": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unpaired_r1.fastq`, example: `unpaired_read_1.fastq`. Output file for unpired read 1", - "help_text": "Type: `file`, default: `$id.$key.unpaired_r1.fastq`, example: `unpaired_read_1.fastq`. Output file for unpired read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.unpaired_r1.fastq" - } - - - , - "unpaired_r2": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.unpaired_r2.fastq`, example: `unpaired_read_2.fastq`. Output file for unpaired read 2", - "help_text": "Type: `file`, default: `$id.$key.unpaired_r2.fastq`, example: `unpaired_read_2.fastq`. Output file for unpaired read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists." - , - "default":"$id.$key.unpaired_r2.fastq" - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "trimgalore", + "description": "A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. \n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "array", + "items": { + "type": "string" + }, + "format": "path", + "exists": true, + "description": "Input files", + "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample1_r1.fq;sample1_r2.fq;sample2_r1.fq;sample2_r2.fq\"]`. " + } + } }, - - { - "$ref": "#/definitions/trimming options" + "trimming options": { + "title": "Trimming options", + "type": "object", + "description": "No description", + "properties": { + "quality": { + "type": "integer", + "description": "Trim low-quality ends (below the specified Phred score) from reads in addition to adapter removal", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "phred33": { + "type": "boolean", + "description": "Instructs Cutadapt to use ASCII+33 quality scores as Phred scores (Sanger/Illumina 1.9+ encoding) for quality trimming.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "phred64": { + "type": "boolean", + "description": "Instructs Cutadapt to use ASCII+64 quality scores as Phred scores (Illumina 1.5 encoding) for quality trimming.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fastqc": { + "type": "boolean", + "description": "Run FastQC in the default mode on the FastQ file once trimming is complete.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "fastqc_args": { + "type": "string", + "description": "Passes extra arguments (excluding files) to FastQC", + "help_text": "Type: `string`, multiple: `False`, example: `\"--nogroup --noextract\"`. " + }, + "fastqc_contaminants": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains the list of contaminants for FastQC to screen overrepresented sequences against", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"contaminants.txt\"`. " + }, + "fastqc_adapters": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains the list of adapter sequences which which FasstQC will explicity search against the library", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"adapters.txt\"`. " + }, + "fastqc_limits": { + "type": "string", + "format": "path", + "description": "Specifies a non-default file which contains a set of criteria which FastQC will use to determine the warn/error limits for the various modules", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"limits.txt\"`. " + }, + "adapter": { + "type": "string", + "description": "Adapter sequence to be trimmed", + "help_text": "Type: `string`, multiple: `False`, example: `\"AGCTCCCG\"`. " + }, + "adapter2": { + "type": "string", + "description": "Optional adapter sequence to be trimmed off read 2 of paired-end files", + "help_text": "Type: `string`, multiple: `False`, example: `\"AGCTCCCG\"`. " + }, + "illumina": { + "type": "boolean", + "description": "Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "stranded_illumina": { + "type": "boolean", + "description": "Adapter sequence to be trimmed is the first 13bp of the Illumina stranded mRNA or Total RNA adapter 'ACTGTCTCTTATA' instead of the default auto-detection of adapter sequence.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "nextera": { + "type": "boolean", + "description": "Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "small_rna": { + "type": "boolean", + "description": "Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "consider_already_trimmed": { + "type": "integer", + "description": "During adapter auto-detection, the limit set by this argument allows the user to set a threshold up to which the file is considered already adapter-trimmed", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "max_length": { + "type": "integer", + "description": "Discard reads that are longer than the specified value after trimming", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "stringency": { + "type": "integer", + "description": "Overlap with adapter sequence required to trim a sequence", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "error_rate": { + "type": "number", + "description": "Maximum allowed error rate (no", + "help_text": "Type: `double`, multiple: `False`, example: `0.1`. " + }, + "gzip": { + "type": "boolean", + "description": "Compress the output file with GZIP", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "dont_gzip": { + "type": "boolean", + "description": "Output files won't be compressed with GZIP", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "length": { + "type": "integer", + "description": "Discard reads that became shorter than the specified length because of either quality or adapter trimming", + "help_text": "Type: `integer`, multiple: `False`, example: `20`. " + }, + "max_n": { + "type": "integer", + "description": "The total number of Ns a read may contain before it will be removed altogether.In a paired-end setting, either read exceeding this limit will result in the entire pair being removed from the trimmed output files", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "trim_n": { + "type": "boolean", + "description": "Removes Ns from either side of the read", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "no_report_file": { + "type": "boolean", + "description": "If specified no report file will be generated.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "suppress_warn": { + "type": "boolean", + "description": "If specified any output to STDOUT or STDERR will be suppressed.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "clip_R1": { + "type": "integer", + "description": "Instructs TrimGalore to remove given number of bp from the 5' end of read 1 (or single-end reads)", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "clip_R2": { + "type": "integer", + "description": "Instructs TrimGalore to remove given number bp from the 5' end of read 2 (paired-end reads only)", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "three_prime_clip_R1": { + "type": "integer", + "description": "Instructs Trim Galore to remove spacified number of bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "three_prime_clip_R2": { + "type": "integer", + "description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "nextseq": { + "type": "integer", + "description": "This enables the option '--nextseq-trim=3'CUTOFF' within Cutadapt, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "basename": { + "type": "string", + "description": "Use specified name (PREFERRED_NAME) as the basename for output files, instead of deriving the filenames from the input files", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/specific trimming options without adapter/quality trimming" + "specific trimming options without adapter/quality trimming": { + "title": "Specific trimming options without adapter/quality trimming", + "type": "object", + "description": "No description", + "properties": { + "hardtrim5": { + "type": "integer", + "description": "Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to bp at the 5'-end", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "hardtrim3": { + "type": "integer", + "description": "Instead of performing adapter-/quality trimming, this option will simply hard-trim sequences to bp at the 3'-end", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "clock": { + "type": "boolean", + "description": "In this mode, reads are trimmed in a specific way that is currently used for the Mouse Epigenetic Clock.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "polyA": { + "type": "boolean", + "description": "This is a new, still experimental, trimming mode to identify and remove poly-A tails from sequences", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "implicon": { + "type": "boolean", + "description": "This is a special mode of operation for paired-end data, such as required for the IMPLICON method, where a UMI sequence is getting transferred from the start of Read 2 to the readID of both reads", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/rrbs-specific options" + "rrbs-specific options": { + "title": "RRBS-specific options", + "type": "object", + "description": "No description", + "properties": { + "rrbs": { + "type": "boolean", + "description": "Specifies that the input file was an MspI digested RRBS sample (recognition site is CCGG)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "non_directional": { + "type": "boolean", + "description": "Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "keep": { + "type": "boolean", + "description": "Keep the quality trimmed intermediate file.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/paired-end specific options" + "paired-end specific options": { + "title": "Paired-end specific options", + "type": "object", + "description": "No description", + "properties": { + "paired": { + "type": "boolean", + "description": "This option performs length trimming of quality/adapter/RRBS trimmed reads for paired-end files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "retain_unpaired": { + "type": "boolean", + "description": "If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "length_1": { + "type": "integer", + "description": "Unpaired single-end read length cutoff needed for read 1 to be written to '.unpaired_1.fq' output file", + "help_text": "Type: `integer`, multiple: `False`, example: `35`. " + }, + "length_2": { + "type": "integer", + "description": "Unpaired single-end read length cutoff needed for read 2 to be written to '.unpaired_2.fq' output file", + "help_text": "Type: `integer`, multiple: `False`, example: `35`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output_dir": { + "type": "string", + "format": "path", + "description": "If specified all output will be written to this directory instead of the current directory.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"trimmed_output\"`, direction: `output`. ", + "default": "trimmed_output" + }, + "trimmed_r1": { + "type": "string", + "format": "path", + "description": "Output file for read 1", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_r1.fastq\"`, direction: `output`, example: `\"read_1.fastq\"`. ", + "default": "$id.$key.trimmed_r1.fastq" + }, + "trimmed_r2": { + "type": "string", + "format": "path", + "description": "Output file for read 2", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_r2.fastq\"`, direction: `output`, example: `\"read_2.fastq\"`. ", + "default": "$id.$key.trimmed_r2.fastq" + }, + "trimming_report_r1": { + "type": "string", + "format": "path", + "description": "Trimming report for read 1", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimming_report_r1.txt\"`, direction: `output`, example: `\"read_1.trimming_report.txt\"`. ", + "default": "$id.$key.trimming_report_r1.txt" + }, + "trimming_report_r2": { + "type": "string", + "format": "path", + "description": "Trimming report for read 1", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimming_report_r2.txt\"`, direction: `output`, example: `\"read_2.trimming_report.txt\"`. ", + "default": "$id.$key.trimming_report_r2.txt" + }, + "trimmed_fastqc_html_1": { + "type": "string", + "format": "path", + "description": "FastQC report for trimmed (single-end) reads (or read 1 for paired-end)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_fastqc_html_1.html\"`, direction: `output`, example: `\"read_1.fastqc.html\"`. ", + "default": "$id.$key.trimmed_fastqc_html_1.html" + }, + "trimmed_fastqc_html_2": { + "type": "string", + "format": "path", + "description": "FastQC report for trimmed reads (read2 for paired-end)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_fastqc_html_2.html\"`, direction: `output`, example: `\"read_2.fastqc.html\"`. ", + "default": "$id.$key.trimmed_fastqc_html_2.html" + }, + "trimmed_fastqc_zip_1": { + "type": "string", + "format": "path", + "description": "FastQC results for trimmed (single-end) reads (or read 1 for paired-end)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_fastqc_zip_1.zip\"`, direction: `output`, example: `\"read_1.fastqc.zip\"`. ", + "default": "$id.$key.trimmed_fastqc_zip_1.zip" + }, + "trimmed_fastqc_zip_2": { + "type": "string", + "format": "path", + "description": "FastQC results for trimmed reads (read2 for paired-end)", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.trimmed_fastqc_zip_2.zip\"`, direction: `output`, example: `\"read_2.fastqc.zip\"`. ", + "default": "$id.$key.trimmed_fastqc_zip_2.zip" + }, + "unpaired_r1": { + "type": "string", + "format": "path", + "description": "Output file for unpired read 1", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unpaired_r1.fastq\"`, direction: `output`, example: `\"unpaired_read_1.fastq\"`. ", + "default": "$id.$key.unpaired_r1.fastq" + }, + "unpaired_r2": { + "type": "string", + "format": "path", + "description": "Output file for unpaired read 2", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.unpaired_r2.fastq\"`, direction: `output`, example: `\"unpaired_read_2.fastq\"`. ", + "default": "$id.$key.unpaired_r2.fastq" + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/trimming options" + }, + { + "$ref": "#/$defs/specific trimming options without adapter/quality trimming" + }, + { + "$ref": "#/$defs/rrbs-specific options" + }, + { + "$ref": "#/$defs/paired-end specific options" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml index 30a6e66a..93d94197 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -8,13 +8,8 @@ authors: - "maintainer" info: links: - email: "emma@data-intuitive.com" github: "emmarousseau" linkedin: "emmarousseau1" - organizations: - - name: "Data Intuitive" - href: "https://www.data-intuitive.com" - role: "Bioinformatician" argument_groups: - name: "Inputs" arguments: @@ -614,9 +609,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -641,6 +636,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 76059a0c..9e378007 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3045,17 +3045,9 @@ meta = [ ], "info" : { "links" : { - "email" : "emma@data-intuitive.com", "github" : "emmarousseau", "linkedin" : "emmarousseau1" - }, - "organizations" : [ - { - "name" : "Data Intuitive", - "href" : "https://www.data-intuitive.com", - "role" : "Bioinformatician" - } - ] + } } } ], @@ -3717,9 +3709,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3735,6 +3727,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json index 979543bd..50c50bfd 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json @@ -1,635 +1,373 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "umi_tools_dedup", -"description": "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n", -"type": "object", -"definitions": { - - - - "inputs" : { - "title": "Inputs", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required. Input BAM or SAM file", - "help_text": "Type: `file`, required. Input BAM or SAM file. Use --in_sam to specify SAM format." - - } - - - , - "in_sam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, inputs are assumed to be in BAM format", - "help_text": "Type: `boolean_true`, default: `false`. By default, inputs are assumed to be in BAM format. Use this options to specify the use of SAM\nformat for input.\n" - , - "default":false - } - - - , - "bai": { - "type": - "string", - "description": "Type: `file`. BAM index", - "help_text": "Type: `file`. BAM index" - - } - - - , - "random_seed": { - "type": - "integer", - "description": "Type: `integer`. Random seed to initialize number generator with", - "help_text": "Type: `integer`. Random seed to initialize number generator with." - - } - - -} -}, - - - "outputs" : { - "title": "Outputs", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Deduplicated BAM file." - , - "default":"$id.$key.output" - } - - - , - "out_sam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, outputa are written in BAM format", - "help_text": "Type: `boolean_true`, default: `false`. By default, outputa are written in BAM format. Use this options to specify the use of SAM format\nfor output.\n" - , - "default":false - } - - - , - "paired": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. BAM is paired end - output both read pairs", - "help_text": "Type: `boolean_true`, default: `false`. BAM is paired end - output both read pairs. This will also force the use of the template length\nto determine reads with the same mapping coordinates.\n" - , - "default":false - } - - - , - "output_stats": { - "type": - "string", - "description": "Type: `string`. Generate files containing UMI based deduplication statistics files with this prefix in the file names", - "help_text": "Type: `string`. Generate files containing UMI based deduplication statistics files with this prefix in the file names.\n" - - } - - - , - "extract_umi_method": { - "type": - "string", - "description": "Type: `string`, example: `read_id`, choices: ``read_id`, `tag`, `umis``. Specify the method by which the barcodes were encoded in the read", - "help_text": "Type: `string`, example: `read_id`, choices: ``read_id`, `tag`, `umis``. Specify the method by which the barcodes were encoded in the read.\nThe options are:\n * read_id (default) \n * tag\n * umis\n", - "enum": ["read_id", "tag", "umis"] - - - } - - - , - "umi_tag": { - "type": - "string", - "description": "Type: `string`. The tag containing the UMI sequence", - "help_text": "Type: `string`. The tag containing the UMI sequence. This is only required if the extract_umi_method is set to tag.\n" - - } - - - , - "umi_separator": { - "type": - "string", - "description": "Type: `string`, example: `_`. The separator used to separate the UMI from the read sequence", - "help_text": "Type: `string`, example: `_`. The separator used to separate the UMI from the read sequence. This is only required if the\nextract_umi_method is set to id_read. Default: `_`.\n" - - } - - - , - "umi_tag_split": { - "type": - "string", - "description": "Type: `string`. Separate the UMI in tag by \u003cSPLIT\u003e and take the first element", - "help_text": "Type: `string`. Separate the UMI in tag by \u003cSPLIT\u003e and take the first element." - - } - - - , - "umi_tag_delimiter": { - "type": - "string", - "description": "Type: `string`. Separate the UMI in by \u003cDELIMITER\u003e and concatenate the elements", - "help_text": "Type: `string`. Separate the UMI in by \u003cDELIMITER\u003e and concatenate the elements." - - } - - - , - "cell_tag": { - "type": - "string", - "description": "Type: `string`. The tag containing the cell barcode sequence", - "help_text": "Type: `string`. The tag containing the cell barcode sequence. This is only required if the extract_umi_method\nis set to tag.\n" - - } - - - , - "cell_tag_split": { - "type": - "string", - "description": "Type: `string`. Separate the cell barcode in tag by \u003cSPLIT\u003e and take the first element", - "help_text": "Type: `string`. Separate the cell barcode in tag by \u003cSPLIT\u003e and take the first element." - - } - - - , - "cell_tag_delimiter": { - "type": - "string", - "description": "Type: `string`. Separate the cell barcode in by \u003cDELIMITER\u003e and concatenate the elements", - "help_text": "Type: `string`. Separate the cell barcode in by \u003cDELIMITER\u003e and concatenate the elements." - - } - - -} -}, - - - "grouping options" : { - "title": "Grouping Options", - "type": "object", - "description": "No description", - "properties": { - - - "method": { - "type": - "string", - "description": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. The method to use for grouping reads", - "help_text": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. The method to use for grouping reads. \nThe options are: \n * unique\n * percentile\n * cluster\n * adjacency\n * directional (default)\n", - "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] - - - } - - - , - "edit_distance_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `1`. For the adjacency and cluster methods the threshold for the edit distance to connect two\nUMIs in the network can be increased", - "help_text": "Type: `integer`, example: `1`. For the adjacency and cluster methods the threshold for the edit distance to connect two\nUMIs in the network can be increased. The default value of 1 works best unless the UMI is\nvery long (\u003e14bp). Default: `1`.\n" - - } - - - , - "spliced_is_unique": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Causes two reads that start in the same position on the same strand and having the same UMI\nto be considered unique if one is spliced and the other is not", - "help_text": "Type: `boolean_true`, default: `false`. Causes two reads that start in the same position on the same strand and having the same UMI\nto be considered unique if one is spliced and the other is not. (Uses the \u0027N\u0027 cigar operation\nto test for splicing).\n" - , - "default":false - } - - - , - "soft_clip_threshold": { - "type": - "integer", - "description": "Type: `integer`, example: `4`. Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only\na small overhang over the exon junction", - "help_text": "Type: `integer`, example: `4`. Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only\na small overhang over the exon junction. By setting this option, you can treat reads with at\nleast this many bases soft-clipped at the 3\u0027 end as spliced. Default: `4`.\n" - - } - - - , - "multimapping_detection_method": { - "type": - "string", - "description": "Type: `string`. If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting\nthe best read at a given loci", - "help_text": "Type: `string`. If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting\nthe best read at a given loci. Supported tags are `NH`, `X0` and `XT`. If not specified, the read\nwith the highest mapping quality will be selected.\n" - - } - - - , - "read_length": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Use the read length as a criteria when deduping, for e", - "help_text": "Type: `boolean_true`, default: `false`. Use the read length as a criteria when deduping, for e.g. sRNA-Seq." - , - "default":false - } - - -} -}, - - - "single-cell rna-seq options" : { - "title": "Single-cell RNA-Seq Options", - "type": "object", - "description": "No description", - "properties": { - - - "per_gene": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Reads will be grouped together if they have the same gene", - "help_text": "Type: `boolean_true`, default: `false`. Reads will be grouped together if they have the same gene. This is useful if your library prep\ngenerates PCR duplicates with non identical alignment positions such as CEL-Seq. Note this option\nis hardcoded to be on with the count command. I.e. counting is always performed per-gene. Must be\ncombined with either --gene_tag or --per_contig option.\n" - , - "default":false - } - - - , - "gene_tag": { - "type": - "string", - "description": "Type: `string`. Deduplicate per gene", - "help_text": "Type: `string`. Deduplicate per gene. The gene information is encoded in the bam read tag specified.\n" - - } - - - , - "assigned_status_tag": { - "type": - "string", - "description": "Type: `string`. BAM tag which describes whether a read is assigned to a gene", - "help_text": "Type: `string`. BAM tag which describes whether a read is assigned to a gene. Defaults to the same value as given\nfor --gene_tag.\n" - - } - - - , - "skip_tags_regex": { - "type": - "string", - "description": "Type: `string`. Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches\nthis regex", - "help_text": "Type: `string`. Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches\nthis regex. Default (\"^[__|Unassigned]\") matches anything which starts with \"__\" or \"Unassigned\".\n" - - } - - - , - "per_contig": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Deduplicate per contig (field 3 in BAM; RNAME)", - "help_text": "Type: `boolean_true`, default: `false`. Deduplicate per contig (field 3 in BAM; RNAME). All reads with the sam contig will be considered to\nhave the same alignment position. This is useful if you have aligned to a reference transcriptome\nwith one transcript per gene. If you have aligned to a transcriptome with more than one transcript\nper gene, you can supply a map between transcripts and gene using the --gene_transcript_map option.\n" - , - "default":false - } - - - , - "gene_transcript_map": { - "type": - "string", - "description": "Type: `file`. A file containing a mapping between gene names and transcript names", - "help_text": "Type: `file`. A file containing a mapping between gene names and transcript names. The file should be tab\nseparated with the gene name in the first column and the transcript name in the second column.\n" - - } - - - , - "per_cell": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Reads will only be grouped together if they have the same cell barcode", - "help_text": "Type: `boolean_true`, default: `false`. Reads will only be grouped together if they have the same cell barcode. Can be combined with\n--per_gene.\n" - , - "default":false - } - - -} -}, - - - "sam/bam options" : { - "title": "SAM/BAM Options", - "type": "object", - "description": "No description", - "properties": { - - - "mapping_quality": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Minimium mapping quality (MAPQ) for a read to be retained", - "help_text": "Type: `integer`, example: `0`. Minimium mapping quality (MAPQ) for a read to be retained. Default: `0`.\n" - - } - - - , - "unmapped_reads": { - "type": - "string", - "description": "Type: `string`, example: `discard`. How unmapped reads should be handled", - "help_text": "Type: `string`, example: `discard`. How unmapped reads should be handled. \nThe options are:\n * \"discard\": Discard all unmapped reads. (default)\n * \"use\": If read2 is unmapped, deduplicate using read1 only. Requires --paired.\n * \"output\": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.\n" - - } - - - , - "chimeric_pairs": { - "type": - "string", - "description": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How chimeric pairs should be handled", - "help_text": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How chimeric pairs should be handled. \nThe options are:\n * \"discard\": Discard all chimeric read pairs.\n * \"use\": Deduplicate using read1 only. (default)\n * \"output\": Output chimeric pairs without UMI grouping/deduplication. Only available in\n umi_tools group.\n", - "enum": ["discard", "use", "output"] - - - } - - - , - "unpaired_reads": { - "type": - "string", - "description": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How unpaired reads should be handled", - "help_text": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How unpaired reads should be handled. \nThe options are: \n * \"discard\": Discard all unmapped reads.\n * \"use\": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default)\n * \"output\": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available\n in umi_tools group.\n", - "enum": ["discard", "use", "output"] - - - } - - - , - "ignore_umi": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ignore the UMI and group reads using mapping coordinates only", - "help_text": "Type: `boolean_true`, default: `false`. Ignore the UMI and group reads using mapping coordinates only." - , - "default":false - } - - - , - "subset": { - "type": - "number", - "description": "Type: `double`. Only consider a fraction of the reads, chosen at random", - "help_text": "Type: `double`. Only consider a fraction of the reads, chosen at random. This is useful for doing saturation\nanalyses.\n" - - } - - - , - "chrom": { - "type": - "string", - "description": "Type: `string`. Only consider a single chromosome", - "help_text": "Type: `string`. Only consider a single chromosome. This is useful for debugging/testing purposes." - - } - - -} -}, - - - "group/dedup options" : { - "title": "Group/Dedup Options", - "type": "object", - "description": "No description", - "properties": { - - - "no_sort_output": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default, output is sorted", - "help_text": "Type: `boolean_true`, default: `false`. By default, output is sorted. This involves the use of a temporary unsorted file (saved in\n--temp_dir). Use this option to turn off sorting.\n" - , - "default":false - } - - - , - "buffer_whole_contig": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Forces dedup to parse an entire contig before yielding any reads for deduplication", - "help_text": "Type: `boolean_true`, default: `false`. Forces dedup to parse an entire contig before yielding any reads for deduplication. This is the\nonly way to absolutely guarantee that all reads with the same start position are grouped together\nfor deduplication since dedup uses the start position of the read, not the alignment coordinate on\nwhich the reads are sorted. However, by default, dedup reads for another 1000bp before outputting\nread groups which will avoid any reads being missed with short read sequencing (\u003c1000bp).\n" - , - "default":false - } - - -} -}, - - - "common options" : { - "title": "Common Options", - "type": "object", - "description": "No description", - "properties": { - - - "log": { - "type": - "string", - "description": "Type: `file`. File with logging information", - "help_text": "Type: `file`. File with logging information." - - } - - - , - "log2stderr": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Send logging information to stderr", - "help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr." - , - "default":false - } - - - , - "verbose": { - "type": - "integer", - "description": "Type: `integer`, example: `0`. Log level", - "help_text": "Type: `integer`, example: `0`. Log level. The higher, the more output. Default: `0`.\n" - - } - - - , - "error": { - "type": - "string", - "description": "Type: `file`. File with error information", - "help_text": "Type: `file`. File with error information." - - } - - - , - "temp_dir": { - "type": - "string", - "description": "Type: `string`. Directory for temporary files", - "help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.\n" - - } - - - , - "compresslevel": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. Level of Gzip compression to use", - "help_text": "Type: `integer`, example: `6`. Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default.\nDefault: `6`.\n" - - } - - - , - "timeit": { - "type": - "string", - "description": "Type: `file`. Store timing information in file", - "help_text": "Type: `file`. Store timing information in file." - - } - - - , - "timeit_name": { - "type": - "string", - "description": "Type: `string`, example: `all`. Name in timing file for this class of jobs", - "help_text": "Type: `string`, example: `all`. Name in timing file for this class of jobs. Default: `all`.\n" - - } - - - , - "timeit_header": { - "type": - "string", - "description": "Type: `string`. Add header for timing information", - "help_text": "Type: `string`. Add header for timing information." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/inputs" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "umi_tools_dedup", + "description": "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n", + "type": "object", + "$defs": { + "inputs": { + "title": "Inputs", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "Input BAM or SAM file", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "in_sam": { + "type": "boolean", + "description": "By default, inputs are assumed to be in BAM format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "bai": { + "type": "string", + "format": "path", + "description": "BAM index", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "random_seed": { + "type": "integer", + "description": "Random seed to initialize number generator with.", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/outputs" + "outputs": { + "title": "Outputs", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Deduplicated BAM file.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + }, + "out_sam": { + "type": "boolean", + "description": "By default, outputa are written in BAM format", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "paired": { + "type": "boolean", + "description": "BAM is paired end - output both read pairs", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "output_stats": { + "type": "string", + "description": "Generate files containing UMI based deduplication statistics files with this prefix in the file names.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "extract_umi_method": { + "type": "string", + "description": "Specify the method by which the barcodes were encoded in the read.\nThe options are:\n * read_id (default) \n * tag\n * umis\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"read_id\"`, choices: ``read_id`, `tag`, `umis``. ", + "enum": [ + "read_id", + "tag", + "umis" + ] + }, + "umi_tag": { + "type": "string", + "description": "The tag containing the UMI sequence", + "help_text": "Type: `string`, multiple: `False`. " + }, + "umi_separator": { + "type": "string", + "description": "The separator used to separate the UMI from the read sequence", + "help_text": "Type: `string`, multiple: `False`, example: `\"_\"`. " + }, + "umi_tag_split": { + "type": "string", + "description": "Separate the UMI in tag by and take the first element.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "umi_tag_delimiter": { + "type": "string", + "description": "Separate the UMI in by and concatenate the elements.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "cell_tag": { + "type": "string", + "description": "The tag containing the cell barcode sequence", + "help_text": "Type: `string`, multiple: `False`. " + }, + "cell_tag_split": { + "type": "string", + "description": "Separate the cell barcode in tag by and take the first element.", + "help_text": "Type: `string`, multiple: `False`. " + }, + "cell_tag_delimiter": { + "type": "string", + "description": "Separate the cell barcode in by and concatenate the elements.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/grouping options" + "grouping options": { + "title": "Grouping Options", + "type": "object", + "description": "No description", + "properties": { + "method": { + "type": "string", + "description": "The method to use for grouping reads", + "help_text": "Type: `string`, multiple: `False`, example: `\"directional\"`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. ", + "enum": [ + "unique", + "percentile", + "cluster", + "adjacency", + "directional" + ] + }, + "edit_distance_threshold": { + "type": "integer", + "description": "For the adjacency and cluster methods the threshold for the edit distance to connect two\nUMIs in the network can be increased", + "help_text": "Type: `integer`, multiple: `False`, example: `1`. " + }, + "spliced_is_unique": { + "type": "boolean", + "description": "Causes two reads that start in the same position on the same strand and having the same UMI\nto be considered unique if one is spliced and the other is not", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "soft_clip_threshold": { + "type": "integer", + "description": "Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only\na small overhang over the exon junction", + "help_text": "Type: `integer`, multiple: `False`, example: `4`. " + }, + "multimapping_detection_method": { + "type": "string", + "description": "If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting\nthe best read at a given loci", + "help_text": "Type: `string`, multiple: `False`. " + }, + "read_length": { + "type": "boolean", + "description": "Use the read length as a criteria when deduping, for e.g", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/single-cell rna-seq options" + "single-cell rna-seq options": { + "title": "Single-cell RNA-Seq Options", + "type": "object", + "description": "No description", + "properties": { + "per_gene": { + "type": "boolean", + "description": "Reads will be grouped together if they have the same gene", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gene_tag": { + "type": "string", + "description": "Deduplicate per gene", + "help_text": "Type: `string`, multiple: `False`. " + }, + "assigned_status_tag": { + "type": "string", + "description": "BAM tag which describes whether a read is assigned to a gene", + "help_text": "Type: `string`, multiple: `False`. " + }, + "skip_tags_regex": { + "type": "string", + "description": "Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches\nthis regex", + "help_text": "Type: `string`, multiple: `False`. " + }, + "per_contig": { + "type": "boolean", + "description": "Deduplicate per contig (field 3 in BAM; RNAME)", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "gene_transcript_map": { + "type": "string", + "format": "path", + "description": "A file containing a mapping between gene names and transcript names", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "per_cell": { + "type": "boolean", + "description": "Reads will only be grouped together if they have the same cell barcode", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/sam/bam options" + "sam/bam options": { + "title": "SAM/BAM Options", + "type": "object", + "description": "No description", + "properties": { + "mapping_quality": { + "type": "integer", + "description": "Minimium mapping quality (MAPQ) for a read to be retained", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "unmapped_reads": { + "type": "string", + "description": "How unmapped reads should be handled", + "help_text": "Type: `string`, multiple: `False`, example: `\"discard\"`. " + }, + "chimeric_pairs": { + "type": "string", + "description": "How chimeric pairs should be handled", + "help_text": "Type: `string`, multiple: `False`, example: `\"use\"`, choices: ``discard`, `use`, `output``. ", + "enum": [ + "discard", + "use", + "output" + ] + }, + "unpaired_reads": { + "type": "string", + "description": "How unpaired reads should be handled", + "help_text": "Type: `string`, multiple: `False`, example: `\"use\"`, choices: ``discard`, `use`, `output``. ", + "enum": [ + "discard", + "use", + "output" + ] + }, + "ignore_umi": { + "type": "boolean", + "description": "Ignore the UMI and group reads using mapping coordinates only.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "subset": { + "type": "number", + "description": "Only consider a fraction of the reads, chosen at random", + "help_text": "Type: `double`, multiple: `False`. " + }, + "chrom": { + "type": "string", + "description": "Only consider a single chromosome", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/group/dedup options" + "group/dedup options": { + "title": "Group/Dedup Options", + "type": "object", + "description": "No description", + "properties": { + "no_sort_output": { + "type": "boolean", + "description": "By default, output is sorted", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "buffer_whole_contig": { + "type": "boolean", + "description": "Forces dedup to parse an entire contig before yielding any reads for deduplication", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + } + } }, - - { - "$ref": "#/definitions/common options" + "common options": { + "title": "Common Options", + "type": "object", + "description": "No description", + "properties": { + "log": { + "type": "string", + "format": "path", + "description": "File with logging information.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "log2stderr": { + "type": "boolean", + "description": "Send logging information to stderr.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "integer", + "description": "Log level", + "help_text": "Type: `integer`, multiple: `False`, example: `0`. " + }, + "error": { + "type": "string", + "format": "path", + "description": "File with error information.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "temp_dir": { + "type": "string", + "description": "Directory for temporary files", + "help_text": "Type: `string`, multiple: `False`. " + }, + "compresslevel": { + "type": "integer", + "description": "Level of Gzip compression to use", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "timeit": { + "type": "string", + "format": "path", + "description": "Store timing information in file.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "timeit_name": { + "type": "string", + "description": "Name in timing file for this class of jobs", + "help_text": "Type: `string`, multiple: `False`, example: `\"all\"`. " + }, + "timeit_header": { + "type": "string", + "description": "Add header for timing information.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/inputs" + }, + { + "$ref": "#/$defs/outputs" + }, + { + "$ref": "#/$defs/grouping options" + }, + { + "$ref": "#/$defs/single-cell rna-seq options" + }, + { + "$ref": "#/$defs/sam/bam options" + }, + { + "$ref": "#/$defs/group/dedup options" + }, + { + "$ref": "#/$defs/common options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml index 91740683..d0a5e127 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -437,9 +437,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -464,6 +464,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index 8803ac55..ba2fc467 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3529,9 +3529,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3547,6 +3547,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json index e8f0501a..88284bec 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json @@ -1,430 +1,260 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "umi_tools_extract", -"description": "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `sample.fastq`. File containing the input data", - "help_text": "Type: `file`, required, example: `sample.fastq`. File containing the input data." - - } - - - , - "read2_in": { - "type": - "string", - "description": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired)", - "help_text": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired). If provided, a \u003clist of other required arguments\u003e need to be provided." - - } - - - , - "bc_pattern": { - "type": - "string", - "description": "Type: `string`. The UMI barcode pattern to use e", - "help_text": "Type: `string`. The UMI barcode pattern to use e.g. \u0027NNNNNN\u0027 indicates that the first 6 nucleotides \nof the read are from the UMI.\n" - - } - - - , - "bc_pattern2": { - "type": - "string", - "description": "Type: `string`. The UMI barcode pattern to use for read 2", - "help_text": "Type: `string`. The UMI barcode pattern to use for read 2." - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1", - "help_text": "Type: `file`, required, default: `$id.$key.output`. Output file for read 1." - , - "default":"$id.$key.output" - } - - - , - "read2_out": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2", - "help_text": "Type: `file`, default: `$id.$key.read2_out`. Output file for read 2." - , - "default":"$id.$key.read2_out" - } - - - , - "filtered_out": { - "type": - "string", - "description": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file", - "help_text": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file.\n" - - } - - - , - "filtered_out2": { - "type": - "string", - "description": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file", - "help_text": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file.\n" - - } - - -} -}, - - - "extract options" : { - "title": "Extract Options", - "type": "object", - "description": "No description", - "properties": { - - - "extract_method": { - "type": - "string", - "description": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use", - "help_text": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use. Default: `string`.\n", - "enum": ["string", "regex"] - - - } - - - , - "error_correct_cell": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist", - "help_text": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist." - , - "default":false - } - - - , - "whitelist": { - "type": - "string", - "description": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1", - "help_text": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1. If the --error_correct_cell option is not used, this\ncolumn will be ignored.\n" - - } - - - , - "blacklist": { - "type": - "string", - "description": "Type: `file`. BlackWhitelist of cell barcodes to discard", - "help_text": "Type: `file`. BlackWhitelist of cell barcodes to discard." - - } - - - , - "subset_reads": { - "type": - "integer", - "description": "Type: `integer`. Only parse the first N reads", - "help_text": "Type: `integer`. Only parse the first N reads." - - } - - - , - "quality_filter_threshold": { - "type": - "integer", - "description": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold", - "help_text": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold." - - } - - - , - "quality_filter_mask": { - "type": - "string", - "description": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027", - "help_text": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027.\n" - - } - - - , - "quality_encoding": { - "type": - "string", - "description": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding", - "help_text": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding. Choose from:\n * phred33 [33-77]\n * phred64 [64-106]\n * solexa [59-106]\n", - "enum": ["phred33", "phred64", "solexa"] - - - } - - - , - "reconcile_pairs": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile", - "help_text": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile. This enables support for upstream protocols\nwhere read one contains cell barcodes, and the read pairs have been filtered and corrected without regard\nto the read2.\n" - , - "default":false - } - - - , - "three_prime": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead", - "help_text": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead. This option only works with --extract_method=string since 3\u0027 encoding can be specified\nexplicitly with a regex, e.g `.*(?P\u003cumi_1\u003e.{5})$`.\n" - , - "default":false - } - - - , - "ignore_read_pair_suffixes": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes", - "help_text": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is required if the suffixes are not whitespace\nseparated from the rest of the read name.\narguments:\n" - , - "default":false - } - - - , - "umi_separator": { - "type": - "string", - "description": "Type: `string`, example: `_`. The character that separates the UMI in the read name", - "help_text": "Type: `string`, example: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with\nUMI-tools and used other software. Default: `_`\n" - - } - - - , - "grouping_method": { - "type": - "string", - "description": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs", - "help_text": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying\nthe reads with the same mapping position, but treat similar yet nonidentical UMIs differently. Default: `directional`\n", - "enum": ["unique", "percentile", "cluster", "adjacency", "directional"] - - - } - - -} -}, - - - "common options" : { - "title": "Common Options", - "type": "object", - "description": "No description", - "properties": { - - - "log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.log`. File with logging information", - "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information." - , - "default":"$id.$key.log" - } - - - , - "log2stderr": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Send logging information to stderr", - "help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr." - , - "default":false - } - - - , - "verbose": { - "type": - "integer", - "description": "Type: `integer`. Log level", - "help_text": "Type: `integer`. Log level. The higher, the more output." - - } - - - , - "error": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.error`. File with error information", - "help_text": "Type: `file`, default: `$id.$key.error`. File with error information." - , - "default":"$id.$key.error" - } - - - , - "temp_dir": { - "type": - "string", - "description": "Type: `string`. Directory for temporary files", - "help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.\n" - - } - - - , - "compresslevel": { - "type": - "integer", - "description": "Type: `integer`, example: `6`. Level of Gzip compression to use", - "help_text": "Type: `integer`, example: `6`. Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9).\nDefault `6`.\n" - - } - - - , - "timeit": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file", - "help_text": "Type: `file`, default: `$id.$key.timeit`. Store timing information in file." - , - "default":"$id.$key.timeit" - } - - - , - "timeit_name": { - "type": - "string", - "description": "Type: `string`, default: `all`. Name in timing file for this class of jobs", - "help_text": "Type: `string`, default: `all`. Name in timing file for this class of jobs." - , - "default":"all" - } - - - , - "timeit_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add header for timing information", - "help_text": "Type: `boolean_true`, default: `false`. Add header for timing information." - , - "default":false - } - - - , - "random_seed": { - "type": - "integer", - "description": "Type: `integer`. Random seed to initialize number generator with", - "help_text": "Type: `integer`. Random seed to initialize number generator with." - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "umi_tools_extract", + "description": "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "File containing the input data.", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"sample.fastq\"`. " + }, + "read2_in": { + "type": "string", + "format": "path", + "description": "File containing the input data for the R2 reads (if paired)", + "help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"sample_R2.fastq\"`. " + }, + "bc_pattern": { + "type": "string", + "description": "The UMI barcode pattern to use e.g", + "help_text": "Type: `string`, multiple: `False`. " + }, + "bc_pattern2": { + "type": "string", + "description": "The UMI barcode pattern to use for read 2.", + "help_text": "Type: `string`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "Output file for read 1.", + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ", + "default": "$id.$key.output" + }, + "read2_out": { + "type": "string", + "format": "path", + "description": "Output file for read 2.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.read2_out\"`, direction: `output`. ", + "default": "$id.$key.read2_out" + }, + "filtered_out": { + "type": "string", + "format": "path", + "description": "Write out reads not matching regex pattern or cell barcode whitelist to this file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "filtered_out2": { + "type": "string", + "format": "path", + "description": "Write out read pairs not matching regex pattern or cell barcode whitelist to this file.\n", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + } + } }, - - { - "$ref": "#/definitions/extract options" + "extract options": { + "title": "Extract Options", + "type": "object", + "description": "No description", + "properties": { + "extract_method": { + "type": "string", + "description": "UMI pattern to use", + "help_text": "Type: `string`, multiple: `False`, example: `\"string\"`, choices: ``string`, `regex``. ", + "enum": [ + "string", + "regex" + ] + }, + "error_correct_cell": { + "type": "boolean", + "description": "Error correct cell barcodes to the whitelist.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "whitelist": { + "type": "string", + "format": "path", + "description": "Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "blacklist": { + "type": "string", + "format": "path", + "description": "BlackWhitelist of cell barcodes to discard.", + "help_text": "Type: `file`, multiple: `False`, direction: `input`. " + }, + "subset_reads": { + "type": "integer", + "description": "Only parse the first N reads.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "quality_filter_threshold": { + "type": "integer", + "description": "Remove reads where any UMI base quality score falls below this threshold.", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "quality_filter_mask": { + "type": "string", + "description": "If a UMI base has a quality below this threshold, replace the base with 'N'.\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "quality_encoding": { + "type": "string", + "description": "Quality score encoding", + "help_text": "Type: `string`, multiple: `False`, choices: ``phred33`, `phred64`, `solexa``. ", + "enum": [ + "phred33", + "phred64", + "solexa" + ] + }, + "reconcile_pairs": { + "type": "boolean", + "description": "Allow read 2 infile to contain reads not in read 1 infile", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "three_prime": { + "type": "boolean", + "description": "By default the barcode is assumed to be on the 5' end of the read, but use this option to sepecify that it is\non the 3' end instead", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "ignore_read_pair_suffixes": { + "type": "boolean", + "description": "Ignore \"/1\" and \"/2\" read name suffixes", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "umi_separator": { + "type": "string", + "description": "The character that separates the UMI in the read name", + "help_text": "Type: `string`, multiple: `False`, example: `\"_\"`. " + }, + "grouping_method": { + "type": "string", + "description": "Method to use to determine read groups by subsuming those with similar UMIs", + "help_text": "Type: `string`, multiple: `False`, example: `\"directional\"`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. ", + "enum": [ + "unique", + "percentile", + "cluster", + "adjacency", + "directional" + ] + } + } }, - - { - "$ref": "#/definitions/common options" + "common options": { + "title": "Common Options", + "type": "object", + "description": "No description", + "properties": { + "log": { + "type": "string", + "format": "path", + "description": "File with logging information.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log\"`, direction: `output`. ", + "default": "$id.$key.log" + }, + "log2stderr": { + "type": "boolean", + "description": "Send logging information to stderr.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "integer", + "description": "Log level", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "error": { + "type": "string", + "format": "path", + "description": "File with error information.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.error\"`, direction: `output`. ", + "default": "$id.$key.error" + }, + "temp_dir": { + "type": "string", + "description": "Directory for temporary files", + "help_text": "Type: `string`, multiple: `False`. " + }, + "compresslevel": { + "type": "integer", + "description": "Level of Gzip compression to use", + "help_text": "Type: `integer`, multiple: `False`, example: `6`. " + }, + "timeit": { + "type": "string", + "format": "path", + "description": "Store timing information in file.", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.timeit\"`, direction: `output`. ", + "default": "$id.$key.timeit" + }, + "timeit_name": { + "type": "string", + "description": "Name in timing file for this class of jobs.", + "help_text": "Type: `string`, multiple: `False`, default: `\"all\"`. ", + "default": "all" + }, + "timeit_header": { + "type": "boolean", + "description": "Add header for timing information.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "random_seed": { + "type": "integer", + "description": "Random seed to initialize number generator with.", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/extract options" + }, + { + "$ref": "#/$defs/common options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] } diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml index 45f768aa..5acbe9b0 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -259,9 +259,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_prepareforrsem" executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf" viash_version: "0.9.4" - git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60" + git_commit: "ad89f437262d32b7cf7afcdfc31b363fc698e8ca" git_remote: "https://github.com/viash-hub/biobox" - git_tag: "v0.2.0-35-gb0db228" + git_tag: "v0.2.0-36-gad89f43" package_config: name: "biobox" version: "main" @@ -286,6 +286,134 @@ package_config: - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_tag := 'main'" + authors: + - name: "Robrecht Cannoodt" + roles: + - "author" + - "maintainer" + info: + links: + email: "robrecht@data-intuitive.com" + github: "rcannood" + orcid: "0000-0003-3641-729X" + linkedin: "robrechtcannoodt" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Science Engineer" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Angela Oliveira Pisco" + roles: + - "author" + info: + role: "Contributor" + links: + github: "aopisco" + orcid: "0000-0003-0142-2355" + linkedin: "aopisco" + organizations: + - name: "Insitro" + href: "https://insitro.com" + role: "Director of Computational Biology" + - name: "Open Problems" + href: "https://openproblems.bio" + role: "Core Member" + - name: "Dorien Roosen" + roles: + - "author" + info: + links: + email: "dorien@data-intuitive.com" + github: "dorien-er" + linkedin: "dorien-roosen" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Dries Schaumont" + roles: + - "author" + info: + links: + email: "dries@data-intuitive.com" + github: "DriesSchaumont" + orcid: "0000-0002-4389-0440" + linkedin: "dries-schaumont" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist" + - name: "Emma Rousseau" + roles: + - "author" + info: + links: + github: "emmarousseau" + linkedin: "emmarousseau1" + - name: "Jakub Majercik" + roles: + - "author" + info: + links: + email: "jakub@data-intuitive.com" + github: "jakubmajercik" + linkedin: "jakubmajercik" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Bioinformatics Engineer" + - name: "Kai Waldrant" + roles: + - "author" + info: + links: + github: "KaiWaldrant" + orcid: "0009-0003-8555-1361" + linkedin: "kaiwaldrant" + - name: "Leïla Paquay" + roles: + - "author" + info: + links: + github: "Leila011" + linkedin: "leilapaquay" + - name: "Sai Nirmayi Yasa" + roles: + - "author" + info: + links: + github: "sainirmayi" + linkedin: "sai-nirmayi-yasa" + - name: "Theodoro Gasperin Terra Camargo" + roles: + - "author" + info: + links: + email: "theodorogtc@gmail.com" + github: "tgaspe" + linkedin: "theodoro-gasperin-terra-camargo" + - name: "Toni Verbeiren" + roles: + - "author" + info: + links: + github: "tverbeiren" + linkedin: "verbeiren" + organizations: + - name: "Data Intuitive" + href: "https://www.data-intuitive.com" + role: "Data Scientist and CEO" + - name: "Weiwei Schultz" + roles: + - "author" + info: + links: + linkedin: "weiwei-schultz" + organizations: + - name: "Janssen R&D US" + role: "Associate Director Data Sciences" keywords: - "bioinformatics" - "modules" diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf index 5439a7b4..884f7109 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf @@ -3351,9 +3351,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem", "viash_version" : "0.9.4", - "git_commit" : "b0db228825f3441b4651527e8775e8fc87d06e60", + "git_commit" : "ad89f437262d32b7cf7afcdfc31b363fc698e8ca", "git_remote" : "https://github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-35-gb0db228" + "git_tag" : "v0.2.0-36-gad89f43" }, "package_config" : { "name" : "biobox", @@ -3369,6 +3369,220 @@ meta = [ ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", ".engines[.type == 'docker'].target_tag := 'main'" ], + "authors" : [ + { + "name" : "Robrecht Cannoodt", + "roles" : [ + "author", + "maintainer" + ], + "info" : { + "links" : { + "email" : "robrecht@data-intuitive.com", + "github" : "rcannood", + "orcid" : "0000-0003-3641-729X", + "linkedin" : "robrechtcannoodt" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Science Engineer" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Angela Oliveira Pisco", + "roles" : [ + "author" + ], + "info" : { + "role" : "Contributor", + "links" : { + "github" : "aopisco", + "orcid" : "0000-0003-0142-2355", + "linkedin" : "aopisco" + }, + "organizations" : [ + { + "name" : "Insitro", + "href" : "https://insitro.com", + "role" : "Director of Computational Biology" + }, + { + "name" : "Open Problems", + "href" : "https://openproblems.bio", + "role" : "Core Member" + } + ] + } + }, + { + "name" : "Dorien Roosen", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dorien@data-intuitive.com", + "github" : "dorien-er", + "linkedin" : "dorien-roosen" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Dries Schaumont", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "dries@data-intuitive.com", + "github" : "DriesSchaumont", + "orcid" : "0000-0002-4389-0440", + "linkedin" : "dries-schaumont" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist" + } + ] + } + }, + { + "name" : "Emma Rousseau", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "emmarousseau", + "linkedin" : "emmarousseau1" + } + } + }, + { + "name" : "Jakub Majercik", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "jakub@data-intuitive.com", + "github" : "jakubmajercik", + "linkedin" : "jakubmajercik" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Bioinformatics Engineer" + } + ] + } + }, + { + "name" : "Kai Waldrant", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "KaiWaldrant", + "orcid" : "0009-0003-8555-1361", + "linkedin" : "kaiwaldrant" + } + } + }, + { + "name" : "Leïla Paquay", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "Leila011", + "linkedin" : "leilapaquay" + } + } + }, + { + "name" : "Sai Nirmayi Yasa", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "sainirmayi", + "linkedin" : "sai-nirmayi-yasa" + } + } + }, + { + "name" : "Theodoro Gasperin Terra Camargo", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "email" : "theodorogtc@gmail.com", + "github" : "tgaspe", + "linkedin" : "theodoro-gasperin-terra-camargo" + } + } + }, + { + "name" : "Toni Verbeiren", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "github" : "tverbeiren", + "linkedin" : "verbeiren" + }, + "organizations" : [ + { + "name" : "Data Intuitive", + "href" : "https://www.data-intuitive.com", + "role" : "Data Scientist and CEO" + } + ] + } + }, + { + "name" : "Weiwei Schultz", + "roles" : [ + "author" + ], + "info" : { + "links" : { + "linkedin" : "weiwei-schultz" + }, + "organizations" : [ + { + "name" : "Janssen R&D US", + "role" : "Associate Director Data Sciences" + } + ] + } + } + ], "keywords" : [ "bioinformatics", "modules", diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json b/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json index 98b77e2f..d1aeac95 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json @@ -1,234 +1,136 @@ { -"$schema": "http://json-schema.org/draft-07/schema", -"title": "umi_tools_prepareforrsem", -"description": "Make the output from umi-tools dedup or group compatible with RSEM", -"type": "object", -"definitions": { - - - - "input" : { - "title": "Input", - "type": "object", - "description": "No description", - "properties": { - - - "input": { - "type": - "string", - "description": "Type: `file`, required, example: `$id.transcriptome.bam`. ", - "help_text": "Type: `file`, required, example: `$id.transcriptome.bam`. " - - } - - -} -}, - - - "output" : { - "title": "Output", - "type": "object", - "description": "No description", - "properties": { - - - "output": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.output.bam`, example: `$id.transcriptome_sorted.bam`. ", - "help_text": "Type: `file`, default: `$id.$key.output.bam`, example: `$id.transcriptome_sorted.bam`. " - , - "default":"$id.$key.output.bam" - } - - - , - "log": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]", - "help_text": "Type: `file`, default: `$id.$key.log`. File with logging information [default = stdout]." - , - "default":"$id.$key.log" - } - - - , - "error": { - "type": - "string", - "description": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]", - "help_text": "Type: `file`, default: `$id.$key.error`. File with error information [default = stderr]." - , - "default":"$id.$key.error" - } - - - , - "log2stderr": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Send logging information to stderr [default = False]", - "help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr [default = False]." - , - "default":false - } - - - , - "temp_dir": { - "type": - "string", - "description": "Type: `string`. Directory for temporary files", - "help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable \nTMPDIR is used.\n" - - } - - - , - "compresslevel": { - "type": - "integer", - "description": "Type: `integer`. Level of Gzip compression to use", - "help_text": "Type: `integer`. Level of Gzip compression to use. Default (6) matchesGNU gzip rather than python \ngzip default (which is 9).\n" - - } - - -} -}, - - - "options" : { - "title": "Options", - "type": "object", - "description": "No description", - "properties": { - - - "tags": { - "type": - "string", - "description": "Type: `string`, example: `UG,BX`. Comma-seperated list of tags to transfer from read1 to read2 (Default: \u0027UG,BX\u0027)\n", - "help_text": "Type: `string`, example: `UG,BX`. Comma-seperated list of tags to transfer from read1 to read2 (Default: \u0027UG,BX\u0027)\n" - - } - - - , - "sam": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Input and output SAM rather than BAM", - "help_text": "Type: `boolean_true`, default: `false`. Input and output SAM rather than BAM." - , - "default":false - } - - - , - "timeit": { - "type": - "string", - "description": "Type: `string`. Store timeing information in file [none]", - "help_text": "Type: `string`. Store timeing information in file [none].\n" - - } - - - , - "timeit_name": { - "type": - "string", - "description": "Type: `string`. Name in timing file for this class of jobs [all]", - "help_text": "Type: `string`. Name in timing file for this class of jobs [all].\n" - - } - - - , - "timeit_header": { - "type": - "boolean", - "description": "Type: `boolean_true`, default: `false`. Add header for timing information [none]", - "help_text": "Type: `boolean_true`, default: `false`. Add header for timing information [none]." - , - "default":false - } - - - , - "verbose": { - "type": - "integer", - "description": "Type: `integer`. Loglevel [1]", - "help_text": "Type: `integer`. Loglevel [1]. The higher, the more output.\n" - - } - - - , - "random_seed": { - "type": - "integer", - "description": "Type: `integer`. Random seed to initialize number generator with [none]", - "help_text": "Type: `integer`. Random seed to initialize number generator with [none].\n" - - } - - -} -}, - - - "nextflow input-output arguments" : { - "title": "Nextflow input-output arguments", - "type": "object", - "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", - "properties": { - - - "publish_dir": { - "type": - "string", - "description": "Type: `string`, required, example: `output/`. Path to an output directory", - "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." - - } - - - , - "param_list": { - "type": - "string", - "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", - "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", - "hidden": true - - } - - -} -} -}, -"allOf": [ - - { - "$ref": "#/definitions/input" + "$schema": "https://json-schema.org/draft/2020-12/schema", + "title": "umi_tools_prepareforrsem", + "description": "Make the output from umi-tools dedup or group compatible with RSEM", + "type": "object", + "$defs": { + "input": { + "title": "Input", + "type": "object", + "description": "No description", + "properties": { + "input": { + "type": "string", + "format": "path", + "exists": true, + "description": "", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"$id.transcriptome.bam\"`. " + } + } }, - - { - "$ref": "#/definitions/output" + "output": { + "title": "Output", + "type": "object", + "description": "No description", + "properties": { + "output": { + "type": "string", + "format": "path", + "description": "", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.bam\"`, direction: `output`, example: `\"$id.transcriptome_sorted.bam\"`. ", + "default": "$id.$key.output.bam" + }, + "log": { + "type": "string", + "format": "path", + "description": "File with logging information [default = stdout].", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.log\"`, direction: `output`. ", + "default": "$id.$key.log" + }, + "error": { + "type": "string", + "format": "path", + "description": "File with error information [default = stderr].", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.error\"`, direction: `output`. ", + "default": "$id.$key.error" + }, + "log2stderr": { + "type": "boolean", + "description": "Send logging information to stderr [default = False].", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "temp_dir": { + "type": "string", + "description": "Directory for temporary files", + "help_text": "Type: `string`, multiple: `False`. " + }, + "compresslevel": { + "type": "integer", + "description": "Level of Gzip compression to use", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/options" + "options": { + "title": "Options", + "type": "object", + "description": "No description", + "properties": { + "tags": { + "type": "string", + "description": "Comma-seperated list of tags to transfer from read1 to read2 (Default: 'UG,BX')\n", + "help_text": "Type: `string`, multiple: `False`, example: `\"UG,BX\"`. " + }, + "sam": { + "type": "boolean", + "description": "Input and output SAM rather than BAM.", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "timeit": { + "type": "string", + "description": "Store timeing information in file [none].\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "timeit_name": { + "type": "string", + "description": "Name in timing file for this class of jobs [all].\n", + "help_text": "Type: `string`, multiple: `False`. " + }, + "timeit_header": { + "type": "boolean", + "description": "Add header for timing information [none].", + "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", + "default": false + }, + "verbose": { + "type": "integer", + "description": "Loglevel [1]", + "help_text": "Type: `integer`, multiple: `False`. " + }, + "random_seed": { + "type": "integer", + "description": "Random seed to initialize number generator with [none].\n", + "help_text": "Type: `integer`, multiple: `False`. " + } + } }, - - { - "$ref": "#/definitions/nextflow input-output arguments" + "nextflow input-output arguments": { + "title": "Nextflow input-output arguments", + "type": "object", + "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", + "properties": { + "publish_dir": { + "type": "string", + "description": "Path to an output directory.", + "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. " + } + } } -] + }, + "allOf": [ + { + "$ref": "#/$defs/input" + }, + { + "$ref": "#/$defs/output" + }, + { + "$ref": "#/$defs/options" + }, + { + "$ref": "#/$defs/nextflow input-output arguments" + } + ] }