diff --git a/CHANGELOG.md b/CHANGELOG.md index 02bf7439..717ee40c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# biobox x.x.x +# biobox 0.3.0 ## NEW FUNCTIONALITY diff --git a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml index 1801d7e6..dc5fffeb 100644 --- a/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/executable/agat/agat_convert_bed2gff" executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff index 387648a4..21a9a3d6 100755 --- a/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff +++ b/target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff @@ -515,9 +515,9 @@ 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="2024-11-26T14:03:12Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:51Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 21ba9348..c503b95a 100644 --- a/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,9 +225,9 @@ build_info: output: "target/executable/agat/agat_convert_embl2gff" executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff index 164a2da4..034dd7dd 100755 --- a/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff +++ b/target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff @@ -505,9 +505,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 b84bec22..6620ba0c 100644 --- a/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -230,9 +230,9 @@ build_info: output: "target/executable/agat/agat_convert_genscan2gff" executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff index 72179802..af5b1266 100755 --- a/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff +++ b/target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff @@ -514,9 +514,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 a99f943f..e04e9331 100644 --- a/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -186,9 +186,9 @@ build_info: output: "target/executable/agat/agat_convert_mfannot2gff" executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff index fe6e7992..e25f3622 100755 --- a/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff +++ b/target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff @@ -480,9 +480,9 @@ 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="2024-11-26T14:03:25Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 b6a0ad39..adc17a57 100644 --- a/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,9 +228,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2gtf" executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 819632da..69c8d41a 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 @@ -519,9 +519,9 @@ 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="2024-11-26T14:03:12Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 ef265e5c..57b300b1 100644 --- a/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,9 +188,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gff2tsv" executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 5c95cb95..bab0c23f 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 @@ -484,9 +484,9 @@ 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="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 e9eeed46..35c372fb 100644 --- a/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,9 +195,9 @@ build_info: output: "target/executable/agat/agat_convert_sp_gxf2gxf" executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 d09dedbd..524ab4a6 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 @@ -493,9 +493,9 @@ 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="2024-11-26T14:03:25Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 be8165af..096aa701 100644 --- a/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_add_introns/.config.vsh.yaml @@ -186,9 +186,9 @@ build_info: output: "target/executable/agat/agat_sp_add_introns" executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 869a1c73..17894379 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 @@ -479,9 +479,9 @@ 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="2024-11-26T14:03:12Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 9758ea9d..2b8e664b 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 @@ -236,9 +236,9 @@ 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: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 d11b83b4..9ca9bdd9 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 @@ -517,9 +517,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 2f9a663b..5b8a8348 100644 --- a/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -184,9 +184,9 @@ build_info: output: "target/executable/agat/agat_sp_merge_annotations" executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 b7c5d80e..66313326 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 @@ -482,9 +482,9 @@ 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="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 e512da80..6edc7774 100644 --- a/target/executable/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/executable/agat/agat_sp_statistics/.config.vsh.yaml @@ -231,9 +231,9 @@ build_info: output: "target/executable/agat/agat_sp_statistics" executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/agat/agat_sp_statistics/agat_sp_statistics b/target/executable/agat/agat_sp_statistics/agat_sp_statistics index 402cfdae..7158b4c1 100755 --- a/target/executable/agat/agat_sp_statistics/agat_sp_statistics +++ b/target/executable/agat/agat_sp_statistics/agat_sp_statistics @@ -507,9 +507,9 @@ 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="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 78687499..9027e832 100644 --- a/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -227,9 +227,9 @@ build_info: output: "target/executable/agat/agat_sq_stat_basic" executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 f5e8080e..aab33380 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 @@ -507,9 +507,9 @@ 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="2024-11-26T14:03:25Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z" LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/arriba/.config.vsh.yaml b/target/executable/arriba/.config.vsh.yaml index b6ccf902..5b9cba5e 100644 --- a/target/executable/arriba/.config.vsh.yaml +++ b/target/executable/arriba/.config.vsh.yaml @@ -706,9 +706,9 @@ build_info: output: "target/executable/arriba" executable: "target/executable/arriba/arriba" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/arriba/arriba b/target/executable/arriba/arriba index 1ecfc081..61780ae3 100755 --- a/target/executable/arriba/arriba +++ b/target/executable/arriba/arriba @@ -754,9 +754,9 @@ 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="2024-11-26T14:03:15Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z" LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bases2fastq/.config.vsh.yaml b/target/executable/bases2fastq/.config.vsh.yaml index 22feb6cb..1c5f7e08 100644 --- a/target/executable/bases2fastq/.config.vsh.yaml +++ b/target/executable/bases2fastq/.config.vsh.yaml @@ -394,9 +394,9 @@ build_info: output: "target/executable/bases2fastq" executable: "target/executable/bases2fastq/bases2fastq" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bases2fastq/bases2fastq b/target/executable/bases2fastq/bases2fastq index c0c0dff4..d1fcc9c2 100755 --- a/target/executable/bases2fastq/bases2fastq +++ b/target/executable/bases2fastq/bases2fastq @@ -604,9 +604,9 @@ 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="2024-11-26T14:03:26Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:06Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 caccc844..541818f4 100644 --- a/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -368,9 +368,9 @@ build_info: output: "target/executable/bbmap/bbmap_bbsplit" executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit index 29cb63dd..5e631179 100755 --- a/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit @@ -600,9 +600,9 @@ cp -r bbmap/* /usr/local/bin RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-11-26T14:03:15Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z" LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml index d442c704..4cfbe259 100644 --- a/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml @@ -469,9 +469,9 @@ build_info: output: "target/executable/bcftools/bcftools_annotate" executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_annotate/bcftools_annotate b/target/executable/bcftools/bcftools_annotate/bcftools_annotate index 9ffe713c..09cdffc7 100755 --- a/target/executable/bcftools/bcftools_annotate/bcftools_annotate +++ b/target/executable/bcftools/bcftools_annotate/bcftools_annotate @@ -650,9 +650,9 @@ RUN echo "bcftools: \"$(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="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 b6c4be1e..84657444 100644 --- a/target/executable/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_concat/.config.vsh.yaml @@ -335,9 +335,9 @@ build_info: output: "target/executable/bcftools/bcftools_concat" executable: "target/executable/bcftools/bcftools_concat/bcftools_concat" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_concat/bcftools_concat b/target/executable/bcftools/bcftools_concat/bcftools_concat index 00db7dca..f17af7f3 100755 --- a/target/executable/bcftools/bcftools_concat/bcftools_concat +++ b/target/executable/bcftools/bcftools_concat/bcftools_concat @@ -566,9 +566,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat" -LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml index eaff8470..6b1552e2 100644 --- a/target/executable/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_norm/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/executable/bcftools/bcftools_norm" executable: "target/executable/bcftools/bcftools_norm/bcftools_norm" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_norm/bcftools_norm b/target/executable/bcftools/bcftools_norm/bcftools_norm index ba658dbd..3e78cb60 100755 --- a/target/executable/bcftools/bcftools_norm/bcftools_norm +++ b/target/executable/bcftools/bcftools_norm/bcftools_norm @@ -589,9 +589,9 @@ RUN echo "bcftools: \"$(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="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 fca7c569..3c4bd419 100644 --- a/target/executable/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,9 +185,9 @@ build_info: output: "target/executable/bcftools/bcftools_sort" executable: "target/executable/bcftools/bcftools_sort/bcftools_sort" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_sort/bcftools_sort b/target/executable/bcftools/bcftools_sort/bcftools_sort index d6ebb578..2b5f3881 100755 --- a/target/executable/bcftools/bcftools_sort/bcftools_sort +++ b/target/executable/bcftools/bcftools_sort/bcftools_sort @@ -483,9 +483,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort" -LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml index e3e5965d..3cc2973e 100644 --- a/target/executable/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/executable/bcftools/bcftools_stats/.config.vsh.yaml @@ -458,9 +458,9 @@ build_info: output: "target/executable/bcftools/bcftools_stats" executable: "target/executable/bcftools/bcftools_stats/bcftools_stats" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcftools/bcftools_stats/bcftools_stats b/target/executable/bcftools/bcftools_stats/bcftools_stats index 7e3f242a..06a2d5e2 100755 --- a/target/executable/bcftools/bcftools_stats/bcftools_stats +++ b/target/executable/bcftools/bcftools_stats/bcftools_stats @@ -626,9 +626,9 @@ RUN echo "bcftools: \"$(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="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 2082fc62..03da7f15 100644 --- a/target/executable/bcl_convert/.config.vsh.yaml +++ b/target/executable/bcl_convert/.config.vsh.yaml @@ -418,9 +418,9 @@ build_info: output: "target/executable/bcl_convert" executable: "target/executable/bcl_convert/bcl_convert" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bcl_convert/bcl_convert b/target/executable/bcl_convert/bcl_convert index aa38e6a7..c8e2bc66 100755 --- a/target/executable/bcl_convert/bcl_convert +++ b/target/executable/bcl_convert/bcl_convert @@ -599,9 +599,9 @@ 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="2024-11-26T14:03:21Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 24549b78..4b94e028 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 @@ -274,9 +274,9 @@ 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: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 0127fb75..793bbbb8 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 @@ -554,9 +554,9 @@ 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="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 9c182adf..009876f7 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 @@ -1115,9 +1115,9 @@ 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: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 f5330479..f98066ab 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 @@ -954,9 +954,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1) RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis" -LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml index 8611a679..468bb595 100644 --- a/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/executable/bedtools/bedtools_bamtobed" executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed index c83254ee..146ef3fc 100755 --- a/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed +++ b/target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed @@ -522,9 +522,9 @@ RUN echo "bedtools: \"$(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="2024-11-26T14:03:21Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 63dbe271..dbfede3a 100644 --- a/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,9 +187,9 @@ build_info: output: "target/executable/bedtools/bedtools_bamtofastq" executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq index 71bc51c8..c982db9a 100755 --- a/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq +++ b/target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq @@ -483,9 +483,9 @@ 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="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 7b83a3ba..d64b9723 100644 --- a/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,9 +176,9 @@ build_info: output: "target/executable/bedtools/bedtools_bed12tobed6" executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 index d7b541da..4240d74f 100755 --- a/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 +++ b/target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6 @@ -480,9 +480,9 @@ 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="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 ff8c8224..13ea77e9 100644 --- a/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,9 +214,9 @@ build_info: output: "target/executable/bedtools/bedtools_bedtobam" executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam index de3c746c..e908f0bf 100755 --- a/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam +++ b/target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam @@ -496,9 +496,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam" -LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml index fc359028..bad39651 100644 --- a/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,9 +337,9 @@ build_info: output: "target/executable/bedtools/bedtools_genomecov" executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov index 518ba2b9..8a28fb4f 100755 --- a/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools/bedtools_genomecov/bedtools_genomecov @@ -591,9 +591,9 @@ RUN echo "bedtools: \"$(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="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 3d65347b..6fc44a04 100644 --- a/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,9 +232,9 @@ build_info: output: "target/executable/bedtools/bedtools_getfasta" executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta index d7b790df..8211df9a 100755 --- a/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta +++ b/target/executable/bedtools/bedtools_getfasta/bedtools_getfasta @@ -526,9 +526,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta" -LABEL org.opencontainers.image.created="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml index fece412d..b1f46153 100644 --- a/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,9 +273,9 @@ build_info: output: "target/executable/bedtools/bedtools_groupby" executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_groupby/bedtools_groupby b/target/executable/bedtools/bedtools_groupby/bedtools_groupby index 70109689..4ce69b09 100755 --- a/target/executable/bedtools/bedtools_groupby/bedtools_groupby +++ b/target/executable/bedtools/bedtools_groupby/bedtools_groupby @@ -552,9 +552,9 @@ RUN echo "bedtools: \"$(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="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 2206fb1a..f2a79977 100644 --- a/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,9 +410,9 @@ build_info: output: "target/executable/bedtools/bedtools_intersect" executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_intersect/bedtools_intersect b/target/executable/bedtools/bedtools_intersect/bedtools_intersect index a44acc7f..8ae4cfc4 100755 --- a/target/executable/bedtools/bedtools_intersect/bedtools_intersect +++ b/target/executable/bedtools/bedtools_intersect/bedtools_intersect @@ -633,9 +633,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect" -LABEL org.opencontainers.image.created="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_links/.config.vsh.yaml b/target/executable/bedtools/bedtools_links/.config.vsh.yaml index e8899943..bc6afa65 100644 --- a/target/executable/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_links/.config.vsh.yaml @@ -210,9 +210,9 @@ build_info: output: "target/executable/bedtools/bedtools_links" executable: "target/executable/bedtools/bedtools_links/bedtools_links" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_links/bedtools_links b/target/executable/bedtools/bedtools_links/bedtools_links index 05c976fe..22e16dda 100755 --- a/target/executable/bedtools/bedtools_links/bedtools_links +++ b/target/executable/bedtools/bedtools_links/bedtools_links @@ -500,9 +500,9 @@ RUN echo "bedtools: \"$(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="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 2d7af345..5a26354b 100644 --- a/target/executable/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_merge/.config.vsh.yaml @@ -279,9 +279,9 @@ build_info: output: "target/executable/bedtools/bedtools_merge" executable: "target/executable/bedtools/bedtools_merge/bedtools_merge" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_merge/bedtools_merge b/target/executable/bedtools/bedtools_merge/bedtools_merge index d3d4cc73..f54e4ece 100755 --- a/target/executable/bedtools/bedtools_merge/bedtools_merge +++ b/target/executable/bedtools/bedtools_merge/bedtools_merge @@ -558,9 +558,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo" LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge" -LABEL org.opencontainers.image.created="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml index b9ea21de..6554e8fe 100644 --- a/target/executable/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/executable/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/executable/bedtools/bedtools_sort" executable: "target/executable/bedtools/bedtools_sort/bedtools_sort" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/bedtools/bedtools_sort/bedtools_sort b/target/executable/bedtools/bedtools_sort/bedtools_sort index 7c9dd0d2..941312b3 100755 --- a/target/executable/bedtools/bedtools_sort/bedtools_sort +++ b/target/executable/bedtools/bedtools_sort/bedtools_sort @@ -509,9 +509,9 @@ RUN echo "bedtools: \"$(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="2024-11-26T14:03:23Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z" LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 265b78c3..b4a40135 100644 --- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml @@ -158,9 +158,9 @@ build_info: output: "target/executable/busco/busco_download_datasets" executable: "target/executable/busco/busco_download_datasets/busco_download_datasets" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/busco/busco_download_datasets/busco_download_datasets b/target/executable/busco/busco_download_datasets/busco_download_datasets index 756c0da5..939f9f43 100755 --- a/target/executable/busco/busco_download_datasets/busco_download_datasets +++ b/target/executable/busco/busco_download_datasets/busco_download_datasets @@ -475,9 +475,9 @@ 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="2024-11-26T14:03:21Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 49f2eb24..49b5b868 100644 --- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml @@ -145,9 +145,9 @@ build_info: output: "target/executable/busco/busco_list_datasets" executable: "target/executable/busco/busco_list_datasets/busco_list_datasets" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/busco/busco_list_datasets/busco_list_datasets b/target/executable/busco/busco_list_datasets/busco_list_datasets index 52a9ea11..87b4e113 100755 --- a/target/executable/busco/busco_list_datasets/busco_list_datasets +++ b/target/executable/busco/busco_list_datasets/busco_list_datasets @@ -465,9 +465,9 @@ 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="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 d79d0f59..26ea3c53 100644 --- a/target/executable/busco/busco_run/.config.vsh.yaml +++ b/target/executable/busco/busco_run/.config.vsh.yaml @@ -423,9 +423,9 @@ build_info: output: "target/executable/busco/busco_run" executable: "target/executable/busco/busco_run/busco_run" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/busco/busco_run/busco_run b/target/executable/busco/busco_run/busco_run index 8b59bb28..e1f473e9 100755 --- a/target/executable/busco/busco_run/busco_run +++ b/target/executable/busco/busco_run/busco_run @@ -632,9 +632,9 @@ 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="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 ebfdbd8d..f9c27765 100644 --- a/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/executable/cellranger/cellranger_mkref/.config.vsh.yaml @@ -195,9 +195,9 @@ build_info: output: "target/executable/cellranger/cellranger_mkref" executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/cellranger/cellranger_mkref/cellranger_mkref b/target/executable/cellranger/cellranger_mkref/cellranger_mkref index 88a9838a..dc3f7ab4 100755 --- a/target/executable/cellranger/cellranger_mkref/cellranger_mkref +++ b/target/executable/cellranger/cellranger_mkref/cellranger_mkref @@ -481,9 +481,9 @@ 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="2024-11-26T14:03:21Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z" LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cutadapt/.config.vsh.yaml b/target/executable/cutadapt/.config.vsh.yaml index 2c5d7d9e..6eac2dab 100644 --- a/target/executable/cutadapt/.config.vsh.yaml +++ b/target/executable/cutadapt/.config.vsh.yaml @@ -740,9 +740,9 @@ build_info: output: "target/executable/cutadapt" executable: "target/executable/cutadapt/cutadapt" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/cutadapt/cutadapt b/target/executable/cutadapt/cutadapt index 786040da..37d90bf0 100755 --- a/target/executable/cutadapt/cutadapt +++ b/target/executable/cutadapt/cutadapt @@ -831,9 +831,9 @@ 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="2024-11-26T14:03:16Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z" LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/falco/.config.vsh.yaml b/target/executable/falco/.config.vsh.yaml index c5cb3866..bf8cbe6b 100644 --- a/target/executable/falco/.config.vsh.yaml +++ b/target/executable/falco/.config.vsh.yaml @@ -317,9 +317,9 @@ build_info: output: "target/executable/falco" executable: "target/executable/falco/falco" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/falco/falco b/target/executable/falco/falco index ca457d9e..c9a3dd6f 100755 --- a/target/executable/falco/falco +++ b/target/executable/falco/falco @@ -589,9 +589,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component falco" -LABEL org.opencontainers.image.created="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastp/.config.vsh.yaml b/target/executable/fastp/.config.vsh.yaml index 271043fa..2ed2f08c 100644 --- a/target/executable/fastp/.config.vsh.yaml +++ b/target/executable/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/executable/fastp" executable: "target/executable/fastp/fastp" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/fastp/fastp b/target/executable/fastp/fastp index fc987d16..aec9e4e9 100755 --- a/target/executable/fastp/fastp +++ b/target/executable/fastp/fastp @@ -1028,9 +1028,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /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="2024-11-26T14:03:24Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:04Z" LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index e9a4834b..b2e14f8a 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -340,9 +340,9 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index a48c4ac3..aba1d846 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -601,9 +601,9 @@ 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="2024-11-26T14:03:26Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:06Z" LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/featurecounts/.config.vsh.yaml b/target/executable/featurecounts/.config.vsh.yaml index b5371c54..b8c2cfcd 100644 --- a/target/executable/featurecounts/.config.vsh.yaml +++ b/target/executable/featurecounts/.config.vsh.yaml @@ -645,9 +645,9 @@ build_info: output: "target/executable/featurecounts" executable: "target/executable/featurecounts/featurecounts" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/featurecounts/featurecounts b/target/executable/featurecounts/featurecounts index 97ac0c27..3d0983b9 100755 --- a/target/executable/featurecounts/featurecounts +++ b/target/executable/featurecounts/featurecounts @@ -754,9 +754,9 @@ 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="2024-11-26T14:03:11Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:51Z" LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 3ea1361f..ef40cbf3 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -190,9 +190,9 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index 757273bc..9c0de661 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -493,9 +493,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gffread/.config.vsh.yaml b/target/executable/gffread/.config.vsh.yaml index 1a4a5418..6f7ecbfe 100644 --- a/target/executable/gffread/.config.vsh.yaml +++ b/target/executable/gffread/.config.vsh.yaml @@ -685,9 +685,9 @@ build_info: output: "target/executable/gffread" executable: "target/executable/gffread/gffread" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/gffread/gffread b/target/executable/gffread/gffread index b36bfeb5..bedae97f 100755 --- a/target/executable/gffread/gffread +++ b/target/executable/gffread/gffread @@ -807,9 +807,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z" LABEL org.opencontainers.image.source="https://github.com/gpertea/gffread" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 f011e70b..702b8703 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -218,9 +218,9 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index fa8c92dc..838ec13f 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -506,9 +506,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 f39a8671..9e8d6ab2 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -246,9 +246,9 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index fac19244..46f7605e 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -522,9 +522,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z" LABEL org.opencontainers.image.source="https://github.com/pachterlab/kallisto" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 4f958ec0..13dc43f8 100644 --- a/target/executable/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_call/.config.vsh.yaml @@ -507,9 +507,9 @@ build_info: output: "target/executable/lofreq/lofreq_call" executable: "target/executable/lofreq/lofreq_call/lofreq_call" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/lofreq/lofreq_call/lofreq_call b/target/executable/lofreq/lofreq_call/lofreq_call index d97c22a6..a7b4e890 100755 --- a/target/executable/lofreq/lofreq_call/lofreq_call +++ b/target/executable/lofreq/lofreq_call/lofreq_call @@ -656,9 +656,9 @@ 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="2024-11-26T14:03:25Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 24129eaa..3501690d 100644 --- a/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/executable/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/executable/lofreq/lofreq_indelqual" executable: "target/executable/lofreq/lofreq_indelqual/lofreq_indelqual" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual index 73fb21d4..387537d0 100755 --- a/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual +++ b/target/executable/lofreq/lofreq_indelqual/lofreq_indelqual @@ -501,9 +501,9 @@ 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="2024-11-26T14:03:25Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:05Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc/.config.vsh.yaml b/target/executable/multiqc/.config.vsh.yaml index 3463c963..225831b9 100644 --- a/target/executable/multiqc/.config.vsh.yaml +++ b/target/executable/multiqc/.config.vsh.yaml @@ -456,9 +456,9 @@ build_info: output: "target/executable/multiqc" executable: "target/executable/multiqc/multiqc" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/multiqc/multiqc b/target/executable/multiqc/multiqc index b0167fbd..3b25f831 100755 --- a/target/executable/multiqc/multiqc +++ b/target/executable/multiqc/multiqc @@ -637,9 +637,9 @@ 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="2024-11-26T14:03:16Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/nanoplot/.config.vsh.yaml b/target/executable/nanoplot/.config.vsh.yaml index d78ae5e7..1db24a0c 100644 --- a/target/executable/nanoplot/.config.vsh.yaml +++ b/target/executable/nanoplot/.config.vsh.yaml @@ -492,9 +492,9 @@ build_info: output: "target/executable/nanoplot" executable: "target/executable/nanoplot/nanoplot" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/nanoplot/nanoplot b/target/executable/nanoplot/nanoplot index 13fcd9f6..a5526779 100755 --- a/target/executable/nanoplot/nanoplot +++ b/target/executable/nanoplot/nanoplot @@ -661,9 +661,9 @@ 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="2024-11-26T14:03:16Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z" LABEL org.opencontainers.image.source="https://github.com/wdecoster/NanoPlot" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/pear/.config.vsh.yaml b/target/executable/pear/.config.vsh.yaml index f78e09a4..ddfa2de3 100644 --- a/target/executable/pear/.config.vsh.yaml +++ b/target/executable/pear/.config.vsh.yaml @@ -398,9 +398,9 @@ build_info: output: "target/executable/pear" executable: "target/executable/pear/pear" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/pear/pear b/target/executable/pear/pear index 971902dd..15ec8b34 100755 --- a/target/executable/pear/pear +++ b/target/executable/pear/pear @@ -597,9 +597,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/tseemann/PEAR" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 f3bea10c..5e9ed110 100644 --- a/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/executable/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/executable/qualimap/qualimap_rnaseq" executable: "target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq index 015b5ea7..fbe92281 100755 --- a/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq +++ b/target/executable/qualimap/qualimap_rnaseq/qualimap_rnaseq @@ -527,9 +527,9 @@ 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="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:53Z" LABEL org.opencontainers.image.source="https://bitbucket.org/kokonech/qualimap/commits/branch/master" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 34fcfe99..6151faca 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -852,9 +852,9 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 89eca5a6..e60508ae 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -991,9 +991,9 @@ 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="2024-11-26T14:03:12Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 e8ce9a7a..6a4e3891 100644 --- a/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/executable/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/executable/rsem/rsem_prepare_reference" executable: "target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference index b66fb408..d54f8faa 100755 --- a/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference +++ b/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference @@ -656,9 +656,9 @@ 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="2024-11-26T14:03:13Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:52Z" LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 d00058dc..280b60bf 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -175,9 +175,9 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 46f6b28e..12df111e 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 6252e728..16703dc0 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -201,9 +201,9 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 52a1651a..ca87c154 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -488,9 +488,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 b80e9cfe..e2c5ed2a 100644 --- a/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -294,9 +294,9 @@ build_info: output: "target/executable/rseqc/rseqc_inner_distance" executable: "target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance index d589bffd..386ad6f3 100755 --- a/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance +++ b/target/executable/rseqc/rseqc_inner_distance/rseqc_inner_distance @@ -532,9 +532,9 @@ 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="2024-11-26T14:03:18Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/MonashBioinformaticsPlatform/RSeQC" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 bea35883..9a9aa6db 100644 --- a/target/executable/salmon/salmon_index/.config.vsh.yaml +++ b/target/executable/salmon/salmon_index/.config.vsh.yaml @@ -277,9 +277,9 @@ build_info: output: "target/executable/salmon/salmon_index" executable: "target/executable/salmon/salmon_index/salmon_index" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/salmon/salmon_index/salmon_index b/target/executable/salmon/salmon_index/salmon_index index 5fabf100..5bb7aeb9 100755 --- a/target/executable/salmon/salmon_index/salmon_index +++ b/target/executable/salmon/salmon_index/salmon_index @@ -546,9 +546,9 @@ 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="2024-11-26T14:03:22Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 c8eac798..aa5c90c5 100644 --- a/target/executable/salmon/salmon_quant/.config.vsh.yaml +++ b/target/executable/salmon/salmon_quant/.config.vsh.yaml @@ -1173,9 +1173,9 @@ build_info: output: "target/executable/salmon/salmon_quant" executable: "target/executable/salmon/salmon_quant/salmon_quant" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/salmon/salmon_quant/salmon_quant b/target/executable/salmon/salmon_quant/salmon_quant index 5063a554..8339019b 100755 --- a/target/executable/salmon/salmon_quant/salmon_quant +++ b/target/executable/salmon/salmon_quant/salmon_quant @@ -1168,9 +1168,9 @@ 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="2024-11-26T14:03:21Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:01Z" LABEL org.opencontainers.image.source="https://github.com/COMBINE-lab/salmon" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 293555ea..8a00ae2f 100644 --- a/target/executable/samtools/samtools_collate/.config.vsh.yaml +++ b/target/executable/samtools/samtools_collate/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/executable/samtools/samtools_collate" executable: "target/executable/samtools/samtools_collate/samtools_collate" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_collate/samtools_collate b/target/executable/samtools/samtools_collate/samtools_collate index b5d94833..fd96d64e 100755 --- a/target/executable/samtools/samtools_collate/samtools_collate +++ b/target/executable/samtools/samtools_collate/samtools_collate @@ -519,9 +519,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 443fc742..f0645096 100644 --- a/target/executable/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/executable/samtools/samtools_faidx/.config.vsh.yaml @@ -243,9 +243,9 @@ build_info: output: "target/executable/samtools/samtools_faidx" executable: "target/executable/samtools/samtools_faidx/samtools_faidx" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_faidx/samtools_faidx b/target/executable/samtools/samtools_faidx/samtools_faidx index 61600a9f..e3782810 100755 --- a/target/executable/samtools/samtools_faidx/samtools_faidx +++ b/target/executable/samtools/samtools_faidx/samtools_faidx @@ -512,9 +512,9 @@ 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="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 27f38ac0..4cdf517e 100644 --- a/target/executable/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fasta/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/executable/samtools/samtools_fasta" executable: "target/executable/samtools/samtools_fasta/samtools_fasta" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_fasta/samtools_fasta b/target/executable/samtools/samtools_fasta/samtools_fasta index 7d0ade4d..22c425f0 100755 --- a/target/executable/samtools/samtools_fasta/samtools_fasta +++ b/target/executable/samtools/samtools_fasta/samtools_fasta @@ -625,9 +625,9 @@ 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="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 c5586225..64d1ea21 100644 --- a/target/executable/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/executable/samtools/samtools_fastq/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/executable/samtools/samtools_fastq" executable: "target/executable/samtools/samtools_fastq/samtools_fastq" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_fastq/samtools_fastq b/target/executable/samtools/samtools_fastq/samtools_fastq index d1bb610b..f34a74ec 100755 --- a/target/executable/samtools/samtools_fastq/samtools_fastq +++ b/target/executable/samtools/samtools_fastq/samtools_fastq @@ -626,9 +626,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 d261426e..532c5c1a 100644 --- a/target/executable/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/executable/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/executable/samtools/samtools_flagstat" executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_flagstat/samtools_flagstat b/target/executable/samtools/samtools_flagstat/samtools_flagstat index ebc30680..a9b1bfb2 100755 --- a/target/executable/samtools/samtools_flagstat/samtools_flagstat +++ b/target/executable/samtools/samtools_flagstat/samtools_flagstat @@ -474,9 +474,9 @@ 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="2024-11-26T14:03:18Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 ca8b884b..c6981d2d 100644 --- a/target/executable/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/executable/samtools/samtools_idxstats" executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_idxstats/samtools_idxstats b/target/executable/samtools/samtools_idxstats/samtools_idxstats index 1c56590e..95962259 100755 --- a/target/executable/samtools/samtools_idxstats/samtools_idxstats +++ b/target/executable/samtools/samtools_idxstats/samtools_idxstats @@ -478,9 +478,9 @@ 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="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 156842ac..4cd45f17 100644 --- a/target/executable/samtools/samtools_index/.config.vsh.yaml +++ b/target/executable/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/executable/samtools/samtools_index" executable: "target/executable/samtools/samtools_index/samtools_index" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_index/samtools_index b/target/executable/samtools/samtools_index/samtools_index index f3179b24..946cc145 100755 --- a/target/executable/samtools/samtools_index/samtools_index +++ b/target/executable/samtools/samtools_index/samtools_index @@ -485,9 +485,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 3c2b1676..092019df 100644 --- a/target/executable/samtools/samtools_sort/.config.vsh.yaml +++ b/target/executable/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/executable/samtools/samtools_sort" executable: "target/executable/samtools/samtools_sort/samtools_sort" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_sort/samtools_sort b/target/executable/samtools/samtools_sort/samtools_sort index 64c18981..311a300f 100755 --- a/target/executable/samtools/samtools_sort/samtools_sort +++ b/target/executable/samtools/samtools_sort/samtools_sort @@ -556,9 +556,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 1d4f7bb8..46bc1acb 100644 --- a/target/executable/samtools/samtools_stats/.config.vsh.yaml +++ b/target/executable/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/executable/samtools/samtools_stats" executable: "target/executable/samtools/samtools_stats/samtools_stats" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_stats/samtools_stats b/target/executable/samtools/samtools_stats/samtools_stats index ba11a201..42ef5bae 100755 --- a/target/executable/samtools/samtools_stats/samtools_stats +++ b/target/executable/samtools/samtools_stats/samtools_stats @@ -575,9 +575,9 @@ 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="2024-11-26T14:03:19Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:59Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 61b33a6c..a8bce0fb 100644 --- a/target/executable/samtools/samtools_view/.config.vsh.yaml +++ b/target/executable/samtools/samtools_view/.config.vsh.yaml @@ -665,9 +665,9 @@ build_info: output: "target/executable/samtools/samtools_view" executable: "target/executable/samtools/samtools_view/samtools_view" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/samtools/samtools_view/samtools_view b/target/executable/samtools/samtools_view/samtools_view index 8bb27585..510371d6 100755 --- a/target/executable/samtools/samtools_view/samtools_view +++ b/target/executable/samtools/samtools_view/samtools_view @@ -825,9 +825,9 @@ 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="2024-11-26T14:03:18Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/samtools/samtools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 6ac16aef..2b9094cb 100644 --- a/target/executable/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/executable/seqtk/seqtk_sample" executable: "target/executable/seqtk/seqtk_sample/seqtk_sample" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/seqtk/seqtk_sample/seqtk_sample b/target/executable/seqtk/seqtk_sample/seqtk_sample index a34f9459..d478abc7 100755 --- a/target/executable/seqtk/seqtk_sample/seqtk_sample +++ b/target/executable/seqtk/seqtk_sample/seqtk_sample @@ -481,9 +481,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 6bd98718..e1a1a416 100644 --- a/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/executable/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/executable/seqtk/seqtk_subseq" executable: "target/executable/seqtk/seqtk_subseq/seqtk_subseq" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/seqtk/seqtk_subseq/seqtk_subseq b/target/executable/seqtk/seqtk_subseq/seqtk_subseq index bd0ab089..2fd70a48 100755 --- a/target/executable/seqtk/seqtk_subseq/seqtk_subseq +++ b/target/executable/seqtk/seqtk_subseq/seqtk_subseq @@ -491,9 +491,9 @@ 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="2024-11-26T14:03:16Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z" LABEL org.opencontainers.image.source="https://github.com/lh3/seqtk/tree/v1.4" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sgdemux/.config.vsh.yaml b/target/executable/sgdemux/.config.vsh.yaml index 8c9950a6..6519f639 100644 --- a/target/executable/sgdemux/.config.vsh.yaml +++ b/target/executable/sgdemux/.config.vsh.yaml @@ -429,9 +429,9 @@ build_info: output: "target/executable/sgdemux" executable: "target/executable/sgdemux/sgdemux" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/sgdemux/sgdemux b/target/executable/sgdemux/sgdemux index d1b6a3d2..f0605c73 100755 --- a/target/executable/sgdemux/sgdemux +++ b/target/executable/sgdemux/sgdemux @@ -631,9 +631,9 @@ echo "sgdemux: $(sgdemux --version | cut -d' ' -f2)" > /var/software_versions.tx LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component sgdemux" -LABEL org.opencontainers.image.created="2024-11-26T14:03:20Z" +LABEL org.opencontainers.image.created="2024-12-03T10:34:00Z" LABEL org.opencontainers.image.source="https://github.com/Singular-Genomics/singular-demux" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/snpeff/.config.vsh.yaml b/target/executable/snpeff/.config.vsh.yaml index 53a37577..f2e67d56 100644 --- a/target/executable/snpeff/.config.vsh.yaml +++ b/target/executable/snpeff/.config.vsh.yaml @@ -628,9 +628,9 @@ build_info: output: "target/executable/snpeff" executable: "target/executable/snpeff/snpeff" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/snpeff/snpeff b/target/executable/snpeff/snpeff index 8c9a7112..d03aed8d 100755 --- a/target/executable/snpeff/snpeff +++ b/target/executable/snpeff/snpeff @@ -756,9 +756,9 @@ version_trimmed=$(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="2024-11-26T14:03:16Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z" LABEL org.opencontainers.image.source="https://github.com/pcingola/SnpEff" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 9ae4347c..46c03ed7 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -594,9 +594,9 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index c4f2d4fa..05ea8108 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -740,9 +740,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z" LABEL org.opencontainers.image.source="https://github.com/sortmerna/sortmerna" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 ee3f18b1..3289059c 100644 --- a/target/executable/star/star_align_reads/.config.vsh.yaml +++ b/target/executable/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/executable/star/star_align_reads" executable: "target/executable/star/star_align_reads/star_align_reads" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/star/star_align_reads/star_align_reads b/target/executable/star/star_align_reads/star_align_reads index 805c5632..c650db18 100755 --- a/target/executable/star/star_align_reads/star_align_reads +++ b/target/executable/star/star_align_reads/star_align_reads @@ -1920,9 +1920,9 @@ 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="2024-11-26T14:03:14Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:54Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 c22b2213..caf1333c 100644 --- a/target/executable/star/star_genome_generate/.config.vsh.yaml +++ b/target/executable/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/executable/star/star_genome_generate" executable: "target/executable/star/star_genome_generate/star_genome_generate" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/star/star_genome_generate/star_genome_generate b/target/executable/star/star_genome_generate/star_genome_generate index 027ae05f..6e1f62a4 100755 --- a/target/executable/star/star_genome_generate/star_genome_generate +++ b/target/executable/star/star_genome_generate/star_genome_generate @@ -577,9 +577,9 @@ 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="2024-11-26T14:03:15Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:55Z" LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 5dc503a4..8d9beabd 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -770,9 +770,9 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 8648b0e1..ab00133c 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -881,9 +881,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:56Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 64ffb078..cd74403c 100644 --- a/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,9 +611,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_dedup" executable: "target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 a6670150..676e6b77 100755 --- a/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup +++ b/target/executable/umi_tools/umi_tools_dedup/umi_tools_dedup @@ -770,9 +770,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 3feb56a9..6fc5a531 100644 --- a/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -434,9 +434,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_extract" executable: "target/executable/umi_tools/umi_tools_extract/umi_tools_extract" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 48401358..cde49724 100755 --- a/target/executable/umi_tools/umi_tools_extract/umi_tools_extract +++ b/target/executable/umi_tools/umi_tools_extract/umi_tools_extract @@ -630,9 +630,9 @@ 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="2024-11-26T14:03:17Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:57Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 e275c2ba..f3fa98b5 100644 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -256,9 +256,9 @@ build_info: output: "target/executable/umi_tools/umi_tools_prepareforrsem" executable: "target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 bc966426..fabc416d 100755 --- a/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem +++ b/target/executable/umi_tools/umi_tools_prepareforrsem/umi_tools_prepareforrsem @@ -519,9 +519,9 @@ 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="2024-11-26T14:03:18Z" +LABEL org.opencontainers.image.created="2024-12-03T10:33:58Z" LABEL org.opencontainers.image.source="https://github.com/CGATOxford/UMI-tools" -LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55" +LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" 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 c5dcfb41..cfcb7718 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_bed2gff/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/nextflow/agat/agat_convert_bed2gff" executable: "target/nextflow/agat/agat_convert_bed2gff/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_bed2gff/main.nf b/target/nextflow/agat/agat_convert_bed2gff/main.nf index 7e489240..9d203b76 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/main.nf +++ b/target/nextflow/agat/agat_convert_bed2gff/main.nf @@ -3092,9 +3092,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_bed2gff", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json index fda7e7f6..29e2237c 100644 --- a/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_bed2gff/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -102,7 +102,7 @@ "description": "Type: `boolean_true`, default: `false`. add verbosity", "help_text": "Type: `boolean_true`, default: `false`. add verbosity" , - "default": "False" + "default":false } diff --git a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml index cbc46cbb..a7bd8320 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_embl2gff/.config.vsh.yaml @@ -225,9 +225,9 @@ build_info: output: "target/nextflow/agat/agat_convert_embl2gff" executable: "target/nextflow/agat/agat_convert_embl2gff/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_embl2gff/main.nf b/target/nextflow/agat/agat_convert_embl2gff/main.nf index 47d0e62e..2da07938 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/main.nf +++ b/target/nextflow/agat/agat_convert_embl2gff/main.nf @@ -3085,9 +3085,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_embl2gff", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json index b959bda2..ee3a7899 100644 --- a/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_embl2gff/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } diff --git a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml index 133d92fe..04291ad4 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_genscan2gff/.config.vsh.yaml @@ -230,9 +230,9 @@ build_info: output: "target/nextflow/agat/agat_convert_genscan2gff" executable: "target/nextflow/agat/agat_convert_genscan2gff/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_genscan2gff/main.nf b/target/nextflow/agat/agat_convert_genscan2gff/main.nf index 716e9119..14e03d8e 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/main.nf +++ b/target/nextflow/agat/agat_convert_genscan2gff/main.nf @@ -3087,9 +3087,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_genscan2gff", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json index 4f8d9ed3..0a075d38 100644 --- a/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_genscan2gff/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } @@ -91,7 +91,7 @@ "description": "Type: `boolean_true`, default: `false`. add verbosity", "help_text": "Type: `boolean_true`, default: `false`. add verbosity" , - "default": "False" + "default":false } diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml index a7aee94f..975300c9 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_mfannot2gff/.config.vsh.yaml @@ -186,9 +186,9 @@ build_info: output: "target/nextflow/agat/agat_convert_mfannot2gff" executable: "target/nextflow/agat/agat_convert_mfannot2gff/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf index 90212cf9..a6c8fbaa 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/main.nf +++ b/target/nextflow/agat/agat_convert_mfannot2gff/main.nf @@ -3047,9 +3047,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_mfannot2gff", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json b/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json index f4b1c959..13338e44 100644 --- a/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_mfannot2gff/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.gff.gff" } 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 c3adef68..a949071a 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml @@ -228,9 +228,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2gtf" executable: "target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf index 479c25d8..521ca40f 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf @@ -3068,9 +3068,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2gtf", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 403708d8..06054e77 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gff2gtf/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gtf" } 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 5661b458..7c0bfbb3 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml @@ -188,9 +188,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gff2tsv" executable: "target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf index 16baa1fc..6aea07dd 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/main.nf @@ -3046,9 +3046,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gff2tsv", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 b432323e..09998dc3 100644 --- a/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gff2tsv/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } 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 fa7acd8e..48929ad1 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml @@ -195,9 +195,9 @@ build_info: output: "target/nextflow/agat/agat_convert_sp_gxf2gxf" executable: "target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf index 9777fbd9..1ca00eef 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/main.nf @@ -3046,9 +3046,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_convert_sp_gxf2gxf", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 79b232fd..117ad690 100644 --- a/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json +++ b/target/nextflow/agat/agat_convert_sp_gxf2gxf/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } 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 9fdfde30..826a1b06 100644 --- a/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_add_introns/.config.vsh.yaml @@ -186,9 +186,9 @@ build_info: output: "target/nextflow/agat/agat_sp_add_introns" executable: "target/nextflow/agat/agat_sp_add_introns/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_sp_add_introns/main.nf b/target/nextflow/agat/agat_sp_add_introns/main.nf index 3e30d3f5..e19d0c93 100644 --- a/target/nextflow/agat/agat_sp_add_introns/main.nf +++ b/target/nextflow/agat/agat_sp_add_introns/main.nf @@ -3049,9 +3049,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_add_introns", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 41ad732d..ef12e523 100644 --- a/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_add_introns/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } 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 d42add90..497003e9 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 @@ -236,9 +236,9 @@ 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: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 99b0b374..dbaf11fb 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 @@ -3096,9 +3096,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_filter_feature_from_kill_list", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 190b4aee..7a25e872 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 @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Path to the output GFF file that contains filtered features", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Path to the output GFF file that contains filtered features. \n" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -101,7 +101,7 @@ "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" + "default":false } 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 e89b543e..b9c1b1ee 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_merge_annotations/.config.vsh.yaml @@ -184,9 +184,9 @@ build_info: output: "target/nextflow/agat/agat_sp_merge_annotations" executable: "target/nextflow/agat/agat_sp_merge_annotations/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_sp_merge_annotations/main.nf b/target/nextflow/agat/agat_sp_merge_annotations/main.nf index fe33e0f4..65e7dd1a 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/main.nf +++ b/target/nextflow/agat/agat_sp_merge_annotations/main.nf @@ -3046,9 +3046,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_merge_annotations", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 d864d8fa..3e405d46 100644 --- a/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_merge_annotations/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.gff" } diff --git a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml index d2e8e104..c21f1646 100644 --- a/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sp_statistics/.config.vsh.yaml @@ -231,9 +231,9 @@ build_info: output: "target/nextflow/agat/agat_sp_statistics" executable: "target/nextflow/agat/agat_sp_statistics/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_sp_statistics/main.nf b/target/nextflow/agat/agat_sp_statistics/main.nf index 5da79824..3d7cf01c 100644 --- a/target/nextflow/agat/agat_sp_statistics/main.nf +++ b/target/nextflow/agat/agat_sp_statistics/main.nf @@ -3096,9 +3096,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sp_statistics", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json b/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json index 1e3cacfa..286849d7 100644 --- a/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json +++ b/target/nextflow/agat/agat_sp_statistics/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.output.txt" } @@ -71,7 +71,7 @@ "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" + "default":false } 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 4abbb4b7..b9953201 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml +++ b/target/nextflow/agat/agat_sq_stat_basic/.config.vsh.yaml @@ -227,9 +227,9 @@ build_info: output: "target/nextflow/agat/agat_sq_stat_basic" executable: "target/nextflow/agat/agat_sq_stat_basic/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/agat/agat_sq_stat_basic/main.nf b/target/nextflow/agat/agat_sq_stat_basic/main.nf index 72c25162..291b12db 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/main.nf +++ b/target/nextflow/agat/agat_sq_stat_basic/main.nf @@ -3082,9 +3082,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/agat/agat_sq_stat_basic", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 d72f4d3e..90bd4e80 100644 --- a/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json +++ b/target/nextflow/agat/agat_sq_stat_basic/nextflow_schema.json @@ -60,7 +60,7 @@ "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" + "default":"$id.$key.output.txt" } @@ -81,7 +81,7 @@ "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" + "default":false } diff --git a/target/nextflow/arriba/.config.vsh.yaml b/target/nextflow/arriba/.config.vsh.yaml index 81358ab2..adcc572c 100644 --- a/target/nextflow/arriba/.config.vsh.yaml +++ b/target/nextflow/arriba/.config.vsh.yaml @@ -706,9 +706,9 @@ build_info: output: "target/nextflow/arriba" executable: "target/nextflow/arriba/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/arriba/main.nf b/target/nextflow/arriba/main.nf index fcadc9f0..29fd7d44 100644 --- a/target/nextflow/arriba/main.nf +++ b/target/nextflow/arriba/main.nf @@ -3592,9 +3592,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/arriba", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/arriba/nextflow_schema.json b/target/nextflow/arriba/nextflow_schema.json index bc31a94b..5dc1e112 100644 --- a/target/nextflow/arriba/nextflow_schema.json +++ b/target/nextflow/arriba/nextflow_schema.json @@ -110,7 +110,7 @@ "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" + "default":"$id.$key.fusions.tsv" } @@ -121,7 +121,7 @@ "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" + "default":"$id.$key.fusions_discarded.tsv" } @@ -182,9 +182,7 @@ "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", - "enum": ["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"] - + "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" } @@ -386,7 +384,7 @@ "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" + "default":false } @@ -397,7 +395,7 @@ "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" + "default":false } @@ -408,7 +406,7 @@ "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" + "default":false } diff --git a/target/nextflow/bases2fastq/.config.vsh.yaml b/target/nextflow/bases2fastq/.config.vsh.yaml index 0db4c3e7..803a290f 100644 --- a/target/nextflow/bases2fastq/.config.vsh.yaml +++ b/target/nextflow/bases2fastq/.config.vsh.yaml @@ -394,9 +394,9 @@ build_info: output: "target/nextflow/bases2fastq" executable: "target/nextflow/bases2fastq/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bases2fastq/main.nf b/target/nextflow/bases2fastq/main.nf index c7005030..984a44d2 100644 --- a/target/nextflow/bases2fastq/main.nf +++ b/target/nextflow/bases2fastq/main.nf @@ -3284,9 +3284,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bases2fastq", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bases2fastq/nextflow_schema.json b/target/nextflow/bases2fastq/nextflow_schema.json index 44247bbd..2342a391 100644 --- a/target/nextflow/bases2fastq/nextflow_schema.json +++ b/target/nextflow/bases2fastq/nextflow_schema.json @@ -30,7 +30,7 @@ "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" + "default":false } @@ -41,7 +41,7 @@ "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" + "default":false } @@ -52,7 +52,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -155,7 +155,7 @@ "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" + "default":false } @@ -178,7 +178,7 @@ "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" + "default":false } @@ -189,7 +189,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable project directories\n", "help_text": "Type: `boolean_true`, default: `false`. Disable project directories\n" , - "default": "False" + "default":false } @@ -220,7 +220,7 @@ "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" + "default":false } @@ -251,7 +251,7 @@ "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" + "default":false } @@ -262,7 +262,7 @@ "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" + "default":false } @@ -313,7 +313,7 @@ "description": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Location to save output fastqs", "help_text": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Location to save output fastqs" , - "default": "$id.$key.output_directory.output_directory" + "default":"$id.$key.output_directory.output_directory" } @@ -324,7 +324,7 @@ "description": "Type: `file`, default: `$id.$key.report.report`. Output location for the HTML report", "help_text": "Type: `file`, default: `$id.$key.report.report`. Output location for the HTML report" , - "default": "$id.$key.report.report" + "default":"$id.$key.report.report" } @@ -335,7 +335,7 @@ "description": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Directory containing log files", "help_text": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Directory containing log files" , - "default": "$id.$key.logs.logs" + "default":"$id.$key.logs.logs" } diff --git a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml index 0a4f0f3a..d1152815 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap/bbmap_bbsplit/.config.vsh.yaml @@ -368,9 +368,9 @@ build_info: output: "target/nextflow/bbmap/bbmap_bbsplit" executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bbmap/bbmap_bbsplit/main.nf b/target/nextflow/bbmap/bbmap_bbsplit/main.nf index dbf9c6e5..be42fc55 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap/bbmap_bbsplit/main.nf @@ -3220,9 +3220,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bbmap/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json index 1321e051..e33875e7 100644 --- a/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json +++ b/target/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json @@ -30,7 +30,7 @@ "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" + "default":false } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -92,7 +92,7 @@ "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" + "default":false } @@ -169,7 +169,7 @@ "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" + "default":false } @@ -190,7 +190,7 @@ "description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index", "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n" , - "default": "$id.$key.index.index" + "default":"$id.$key.index.index" } @@ -201,7 +201,7 @@ "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" + "default":"$id.$key.fastq_1.fastq" } @@ -212,7 +212,7 @@ "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" + "default":"$id.$key.fastq_2.fastq" } @@ -223,7 +223,7 @@ "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" + "default":"$id.$key.sam2bam.sh" } @@ -234,7 +234,7 @@ "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" + "default":"$id.$key.scafstats.txt" } @@ -245,7 +245,7 @@ "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" + "default":"$id.$key.refstats.txt" } @@ -256,7 +256,7 @@ "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" + "default":false } diff --git a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml index 8dac336b..0bbc3442 100644 --- a/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_annotate/.config.vsh.yaml @@ -469,9 +469,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_annotate" executable: "target/nextflow/bcftools/bcftools_annotate/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcftools/bcftools_annotate/main.nf b/target/nextflow/bcftools/bcftools_annotate/main.nf index a63131c9..ff2d7bb7 100644 --- a/target/nextflow/bcftools/bcftools_annotate/main.nf +++ b/target/nextflow/bcftools/bcftools_annotate/main.nf @@ -3335,9 +3335,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_annotate", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json index 4bda14e8..c61fa726 100644 --- a/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_annotate/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output annotated file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -101,7 +101,7 @@ "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" + "default":false } @@ -152,7 +152,7 @@ "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" + "default":false } @@ -193,7 +193,7 @@ "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" + "default":false } @@ -300,7 +300,7 @@ "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" + "default":false } diff --git a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml index fbd446a0..55ad2d28 100644 --- a/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_concat/.config.vsh.yaml @@ -335,9 +335,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_concat" executable: "target/nextflow/bcftools/bcftools_concat/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcftools/bcftools_concat/main.nf b/target/nextflow/bcftools/bcftools_concat/main.nf index 9251af84..b08c31f4 100644 --- a/target/nextflow/bcftools/bcftools_concat/main.nf +++ b/target/nextflow/bcftools/bcftools_concat/main.nf @@ -3207,9 +3207,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_concat", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json index acf49c75..5c7ba654 100644 --- a/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_concat/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output concatenated VCF/BCF file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output concatenated VCF/BCF file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -71,7 +71,7 @@ "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" + "default":false } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -105,7 +105,7 @@ "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" + "default":false } @@ -116,7 +116,7 @@ "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" + "default":false } @@ -127,7 +127,7 @@ "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" + "default":false } @@ -138,7 +138,7 @@ "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" + "default":false } @@ -149,7 +149,7 @@ "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" + "default":false } @@ -160,7 +160,7 @@ "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" + "default":false } diff --git a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml index 2a6209bd..1cc23827 100644 --- a/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_norm/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_norm" executable: "target/nextflow/bcftools/bcftools_norm/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcftools/bcftools_norm/main.nf b/target/nextflow/bcftools/bcftools_norm/main.nf index 0a4b015e..b96b07bb 100644 --- a/target/nextflow/bcftools/bcftools_norm/main.nf +++ b/target/nextflow/bcftools/bcftools_norm/main.nf @@ -3300,9 +3300,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_norm", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json index 5bfd9667..26c453b5 100644 --- a/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_norm/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output normalized VCF/BCF file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output normalized VCF/BCF file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -118,7 +118,7 @@ "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" + "default":false } @@ -151,7 +151,7 @@ "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" + "default":false } @@ -162,7 +162,7 @@ "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" + "default":false } @@ -237,7 +237,7 @@ "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" + "default":false } diff --git a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml index e45557b7..2ee5be5f 100644 --- a/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_sort/.config.vsh.yaml @@ -185,9 +185,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_sort" executable: "target/nextflow/bcftools/bcftools_sort/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcftools/bcftools_sort/main.nf b/target/nextflow/bcftools/bcftools_sort/main.nf index 27669366..7973d6d2 100644 --- a/target/nextflow/bcftools/bcftools_sort/main.nf +++ b/target/nextflow/bcftools/bcftools_sort/main.nf @@ -3048,9 +3048,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_sort", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json index 737aeb99..8f06643a 100644 --- a/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_sort/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output sorted VCF/BCF file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml index 7d9f1ccf..79c51a92 100644 --- a/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml +++ b/target/nextflow/bcftools/bcftools_stats/.config.vsh.yaml @@ -458,9 +458,9 @@ build_info: output: "target/nextflow/bcftools/bcftools_stats" executable: "target/nextflow/bcftools/bcftools_stats/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcftools/bcftools_stats/main.nf b/target/nextflow/bcftools/bcftools_stats/main.nf index 2920336e..cd95e4a9 100644 --- a/target/nextflow/bcftools/bcftools_stats/main.nf +++ b/target/nextflow/bcftools/bcftools_stats/main.nf @@ -3337,9 +3337,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcftools/bcftools_stats", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json index 2c35fa3c..88ee92a7 100644 --- a/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json +++ b/target/nextflow/bcftools/bcftools_stats/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output txt statistics file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -91,7 +91,7 @@ "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" + "default":false } @@ -174,7 +174,7 @@ "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" + "default":false } @@ -279,7 +279,7 @@ "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" + "default":false } diff --git a/target/nextflow/bcl_convert/.config.vsh.yaml b/target/nextflow/bcl_convert/.config.vsh.yaml index 0bdd10d3..8e3bc337 100644 --- a/target/nextflow/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/bcl_convert/.config.vsh.yaml @@ -418,9 +418,9 @@ build_info: output: "target/nextflow/bcl_convert" executable: "target/nextflow/bcl_convert/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bcl_convert/main.nf b/target/nextflow/bcl_convert/main.nf index b4807fa1..fa2cffc0 100644 --- a/target/nextflow/bcl_convert/main.nf +++ b/target/nextflow/bcl_convert/main.nf @@ -3329,9 +3329,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bcl_convert", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bcl_convert/nextflow_schema.json b/target/nextflow/bcl_convert/nextflow_schema.json index 5fa9b054..2eec36de 100644 --- a/target/nextflow/bcl_convert/nextflow_schema.json +++ b/target/nextflow/bcl_convert/nextflow_schema.json @@ -240,7 +240,7 @@ "description": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files", "help_text": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files" , - "default": "$id.$key.output_directory.output_directory" + "default":"$id.$key.output_directory.output_directory" } @@ -271,7 +271,7 @@ "description": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory", "help_text": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory" , - "default": "$id.$key.reports.reports" + "default":"$id.$key.reports.reports" } @@ -282,7 +282,7 @@ "description": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory", "help_text": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory" , - "default": "$id.$key.logs.logs" + "default":"$id.$key.logs.logs" } 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 12146241..276857a2 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 @@ -274,9 +274,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 3e35d2fb..c9451404 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_make_reference/main.nf @@ -3146,9 +3146,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_make_reference", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 10a2e002..946d186c 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 @@ -60,7 +60,7 @@ "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" + "default":"$id.$key.reference_archive.gz" } @@ -81,7 +81,7 @@ "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" + "default":"chrM;chrMT;M;MT" } @@ -92,7 +92,7 @@ "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" + "default":false } @@ -103,7 +103,7 @@ "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" + "default":false } 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 55444148..7ef82413 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 @@ -1115,9 +1115,9 @@ build_info: output: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis" executable: "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" 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 cda9fba3..a76bbfa9 100644 --- a/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf +++ b/target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis/main.nf @@ -4193,9 +4193,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bd_rhapsody/bd_rhapsody_sequence_analysis", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 96a2168b..8d89d724 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 @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output_dir.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.output_dir`, example: `output_dir`. The unprocessed output directory containing all the outputs from the pipeline." , - "default": "$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir.output_dir" } @@ -61,7 +61,7 @@ "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" + "default":"$id.$key.output_seurat.rds" } @@ -72,7 +72,7 @@ "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" + "default":"$id.$key.output_mudata.h5mu" } @@ -83,7 +83,7 @@ "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" + "default":"$id.$key.metrics_summary.csv" } @@ -94,7 +94,7 @@ "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" + "default":"$id.$key.pipeline_report.html" } @@ -105,7 +105,7 @@ "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" + "default":"$id.$key.rsec_mols_per_cell.zip" } @@ -116,7 +116,7 @@ "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" + "default":"$id.$key.dbec_mols_per_cell.zip" } @@ -127,7 +127,7 @@ "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" + "default":"$id.$key.rsec_mols_per_cell_unfiltered.zip" } @@ -138,7 +138,7 @@ "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" + "default":"$id.$key.bam.bam" } @@ -149,7 +149,7 @@ "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" + "default":"$id.$key.bam_index.bai" } @@ -160,7 +160,7 @@ "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" + "default":"$id.$key.bioproduct_stats.csv" } @@ -171,7 +171,7 @@ "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" + "default":"$id.$key.dimred_tsne.csv" } @@ -182,7 +182,7 @@ "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" + "default":"$id.$key.dimred_umap.csv" } @@ -193,7 +193,7 @@ "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" + "default":"$id.$key.immune_cell_classification.csv" } @@ -264,7 +264,7 @@ "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" + "default":"$id.$key.sample_tag_metrics.csv" } @@ -275,7 +275,7 @@ "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" + "default":"$id.$key.sample_tag_calls.csv" } @@ -286,7 +286,7 @@ "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" + "default":"$id.$key.sample_tag_counts_*.zip" } @@ -297,7 +297,7 @@ "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" + "default":"$id.$key.sample_tag_counts_unassigned.zip" } @@ -318,7 +318,7 @@ "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" + "default":"$id.$key.vdj_metrics.csv" } @@ -329,7 +329,7 @@ "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" + "default":"$id.$key.vdj_per_cell.csv" } @@ -340,7 +340,7 @@ "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" + "default":"$id.$key.vdj_per_cell_uncorrected.csv" } @@ -351,7 +351,7 @@ "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" + "default":"$id.$key.vdj_dominant_contigs.csv" } @@ -362,7 +362,7 @@ "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" + "default":"$id.$key.vdj_unfiltered_contigs.csv" } @@ -383,7 +383,7 @@ "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" + "default":"$id.$key.atac_metrics.csv" } @@ -394,7 +394,7 @@ "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" + "default":"$id.$key.atac_metrics_json.json" } @@ -405,7 +405,7 @@ "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" + "default":"$id.$key.atac_fragments.gz" } @@ -416,7 +416,7 @@ "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" + "default":"$id.$key.atac_fragments_index.tbi" } @@ -427,7 +427,7 @@ "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" + "default":"$id.$key.atac_transposase_sites.gz" } @@ -438,7 +438,7 @@ "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" + "default":"$id.$key.atac_transposase_sites_index.tbi" } @@ -449,7 +449,7 @@ "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" + "default":"$id.$key.atac_peaks.gz" } @@ -460,7 +460,7 @@ "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" + "default":"$id.$key.atac_peaks_index.tbi" } @@ -471,7 +471,7 @@ "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" + "default":"$id.$key.atac_peak_annotation.gz" } @@ -482,7 +482,7 @@ "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" + "default":"$id.$key.atac_cell_by_peak.zip" } @@ -493,7 +493,7 @@ "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" + "default":"$id.$key.atac_cell_by_peak_unfiltered.zip" } @@ -504,7 +504,7 @@ "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" + "default":"$id.$key.atac_bam.bam" } @@ -515,7 +515,7 @@ "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" + "default":"$id.$key.atac_bam_index.bai" } @@ -536,7 +536,7 @@ "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" + "default":"$id.$key.protein_aggregates_experimental.csv" } @@ -717,7 +717,7 @@ "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" + "default":"sample" } @@ -728,7 +728,7 @@ "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" + "default":false } @@ -789,7 +789,7 @@ "description": "Type: `boolean`, default: `true`. Run jobs in parallel", "help_text": "Type: `boolean`, default: `true`. Run jobs in parallel." , - "default": "True" + "default":true } @@ -800,7 +800,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml index cc00d9ec..c2444185 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtobed/.config.vsh.yaml @@ -235,9 +235,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtobed" executable: "target/nextflow/bedtools/bedtools_bamtobed/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_bamtobed/main.nf b/target/nextflow/bedtools/bedtools_bamtobed/main.nf index 26e4cfd6..f4957ec7 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtobed/main.nf @@ -3101,9 +3101,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtobed", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json index 733d2a87..0c6b2711 100644 --- a/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtobed/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output BED file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -83,7 +83,7 @@ "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" + "default":false } @@ -94,7 +94,7 @@ "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" + "default":false } @@ -105,7 +105,7 @@ "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" + "default":false } @@ -116,7 +116,7 @@ "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" + "default":false } @@ -147,7 +147,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml index b6c876bd..495971a9 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bamtofastq/.config.vsh.yaml @@ -187,9 +187,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bamtofastq" executable: "target/nextflow/bedtools/bedtools_bamtofastq/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf index 68f19766..e2a2821e 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/main.nf +++ b/target/nextflow/bedtools/bedtools_bamtofastq/main.nf @@ -3050,9 +3050,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bamtofastq", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json index 59912ee3..a246cb01 100644 --- a/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bamtofastq/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file", "help_text": "Type: `file`, required, default: `$id.$key.fastq.fastq`. Output FASTQ file." , - "default": "$id.$key.fastq.fastq" + "default":"$id.$key.fastq.fastq" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.fastq2.fastq2`. FASTQ for second end", "help_text": "Type: `file`, default: `$id.$key.fastq2.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.fastq2" + "default":"$id.$key.fastq2.fastq2" } @@ -72,7 +72,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml index f2c5d099..1d509846 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/.config.vsh.yaml @@ -176,9 +176,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bed12tobed6" executable: "target/nextflow/bedtools/bedtools_bed12tobed6/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf index ea8a5ae1..16019625 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/main.nf @@ -3035,9 +3035,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bed12tobed6", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json index 8b50981a..e9118c0f 100644 --- a/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bed12tobed6/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Output BED6 file to be written", "help_text": "Type: `file`, default: `$id.$key.output.output`. Output BED6 file to be written." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml index a44fb3d6..a518d2a1 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_bedtobam/.config.vsh.yaml @@ -214,9 +214,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_bedtobam" executable: "target/nextflow/bedtools/bedtools_bedtobam/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_bedtobam/main.nf b/target/nextflow/bedtools/bedtools_bedtobam/main.nf index f555bea4..17adadae 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/main.nf +++ b/target/nextflow/bedtools/bedtools_bedtobam/main.nf @@ -3083,9 +3083,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_bedtobam", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json index 0654aa9b..fc7e6364 100644 --- a/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_bedtobam/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Output BAM file to be written", "help_text": "Type: `file`, default: `$id.$key.output.output`. Output BAM file to be written." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -71,7 +71,7 @@ "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" + "default":255 } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml index 8b9438c8..49a48c44 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_genomecov/.config.vsh.yaml @@ -337,9 +337,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_genomecov" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_genomecov/main.nf b/target/nextflow/bedtools/bedtools_genomecov/main.nf index 29f1f478..ff93428f 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools/bedtools_genomecov/main.nf @@ -3207,9 +3207,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json index 3e0bb4b2..292d2515 100644 --- a/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json @@ -60,7 +60,7 @@ "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" + "default":"$id.$key.output.bed" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -92,7 +92,7 @@ "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" + "default":false } @@ -103,7 +103,7 @@ "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" + "default":false } @@ -114,7 +114,7 @@ "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" + "default":false } @@ -125,7 +125,7 @@ "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" + "default":false } @@ -136,7 +136,7 @@ "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" + "default":false } @@ -159,7 +159,7 @@ "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" + "default":false } @@ -170,7 +170,7 @@ "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" + "default":false } @@ -181,7 +181,7 @@ "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" + "default":false } @@ -192,7 +192,7 @@ "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" + "default":false } @@ -203,7 +203,7 @@ "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" + "default":false } @@ -234,7 +234,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml index 16492a56..dea43eb2 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_getfasta/.config.vsh.yaml @@ -232,9 +232,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_getfasta" executable: "target/nextflow/bedtools/bedtools_getfasta/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_getfasta/main.nf b/target/nextflow/bedtools/bedtools_getfasta/main.nf index 69d50fa3..d7826b8f 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/main.nf +++ b/target/nextflow/bedtools/bedtools_getfasta/main.nf @@ -3086,9 +3086,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_getfasta", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json index c3f7e079..a543bac3 100644 --- a/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_getfasta/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":false } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -82,7 +82,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file where the output from the \u0027bedtools getfasta\u0027 commend will\nbe written to.\n" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -115,7 +115,7 @@ "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" + "default":false } @@ -126,7 +126,7 @@ "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" + "default":false } @@ -137,7 +137,7 @@ "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" + "default":false } @@ -148,7 +148,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml index 38f06f76..1cdd65d6 100644 --- a/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_groupby/.config.vsh.yaml @@ -273,9 +273,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_groupby" executable: "target/nextflow/bedtools/bedtools_groupby/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_groupby/main.nf b/target/nextflow/bedtools/bedtools_groupby/main.nf index b37d3e70..e473e220 100644 --- a/target/nextflow/bedtools/bedtools_groupby/main.nf +++ b/target/nextflow/bedtools/bedtools_groupby/main.nf @@ -3130,9 +3130,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_groupby", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json b/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json index a4d92e23..c1896c1e 100644 --- a/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_groupby/nextflow_schema.json @@ -40,7 +40,7 @@ "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.$key.output.bed" + "default":"$id.$key.output.bed" } @@ -91,7 +91,7 @@ "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" + "default":false } @@ -102,7 +102,7 @@ "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" + "default":false } @@ -113,7 +113,7 @@ "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" + "default":false } @@ -124,7 +124,7 @@ "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" + "default":false } @@ -135,7 +135,7 @@ "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" + "default":false } @@ -146,7 +146,7 @@ "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" + "default":5 } @@ -157,7 +157,7 @@ "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": "," + "default":"," } diff --git a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml index 9defce46..add5f521 100644 --- a/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_intersect/.config.vsh.yaml @@ -410,9 +410,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_intersect" executable: "target/nextflow/bedtools/bedtools_intersect/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_intersect/main.nf b/target/nextflow/bedtools/bedtools_intersect/main.nf index 57a6745c..06311b92 100644 --- a/target/nextflow/bedtools/bedtools_intersect/main.nf +++ b/target/nextflow/bedtools/bedtools_intersect/main.nf @@ -3282,9 +3282,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_intersect", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json b/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json index add67b19..5345ee1a 100644 --- a/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_intersect/nextflow_schema.json @@ -50,7 +50,7 @@ "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.$key.output.bed" + "default":"$id.$key.output.bed" } @@ -71,7 +71,7 @@ "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" + "default":false } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -115,7 +115,7 @@ "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" + "default":false } @@ -126,7 +126,7 @@ "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" + "default":false } @@ -137,7 +137,7 @@ "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" + "default":false } @@ -148,7 +148,7 @@ "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" + "default":false } @@ -159,7 +159,7 @@ "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" + "default":false } @@ -170,7 +170,7 @@ "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" + "default":false } @@ -181,7 +181,7 @@ "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" + "default":false } @@ -212,7 +212,7 @@ "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" + "default":false } @@ -223,7 +223,7 @@ "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" + "default":false } @@ -234,7 +234,7 @@ "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" + "default":false } @@ -255,7 +255,7 @@ "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" + "default":false } @@ -266,7 +266,7 @@ "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" + "default":false } @@ -287,7 +287,7 @@ "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" + "default":false } @@ -298,7 +298,7 @@ "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" + "default":false } @@ -309,7 +309,7 @@ "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" + "default":false } @@ -320,7 +320,7 @@ "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" + "default":false } @@ -331,7 +331,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml index c9f64ab7..489b4461 100644 --- a/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_links/.config.vsh.yaml @@ -210,9 +210,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_links" executable: "target/nextflow/bedtools/bedtools_links/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_links/main.nf b/target/nextflow/bedtools/bedtools_links/main.nf index 8df0400f..7dfc9e68 100644 --- a/target/nextflow/bedtools/bedtools_links/main.nf +++ b/target/nextflow/bedtools/bedtools_links/main.nf @@ -3073,9 +3073,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_links", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json index 5a468d62..79b6d9b6 100644 --- a/target/nextflow/bedtools/bedtools_links/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_links/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Output HTML file to be written", "help_text": "Type: `file`, default: `$id.$key.output.output`. Output HTML file to be written." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":"http://genome.ucsc.edu" } @@ -72,7 +72,7 @@ "description": "Type: `string`, default: `human`. The organism (e", "help_text": "Type: `string`, default: `human`. The organism (e.g. mouse, human). \n" , - "default": "human" + "default":"human" } @@ -83,7 +83,7 @@ "description": "Type: `string`, default: `hg18`. The genome build", "help_text": "Type: `string`, default: `hg18`. The genome build. \n" , - "default": "hg18" + "default":"hg18" } diff --git a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml index 5e269d5a..fd43b1c2 100644 --- a/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_merge/.config.vsh.yaml @@ -279,9 +279,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_merge" executable: "target/nextflow/bedtools/bedtools_merge/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_merge/main.nf b/target/nextflow/bedtools/bedtools_merge/main.nf index aa247588..fc77ba2f 100644 --- a/target/nextflow/bedtools/bedtools_merge/main.nf +++ b/target/nextflow/bedtools/bedtools_merge/main.nf @@ -3134,9 +3134,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_merge", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json index be7b1f37..77aaf1ab 100644 --- a/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_merge/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output merged file BED to be written", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output merged file BED to be written." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -114,7 +114,7 @@ "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": "," + "default":"," } @@ -135,7 +135,7 @@ "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" + "default":false } @@ -146,7 +146,7 @@ "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" + "default":false } @@ -157,7 +157,7 @@ "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" + "default":false } diff --git a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml index 2cdc8522..66a2fdac 100644 --- a/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml +++ b/target/nextflow/bedtools/bedtools_sort/.config.vsh.yaml @@ -222,9 +222,9 @@ build_info: output: "target/nextflow/bedtools/bedtools_sort" executable: "target/nextflow/bedtools/bedtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/bedtools/bedtools_sort/main.nf b/target/nextflow/bedtools/bedtools_sort/main.nf index fbe6b91e..ed86b7a5 100644 --- a/target/nextflow/bedtools/bedtools_sort/main.nf +++ b/target/nextflow/bedtools/bedtools_sort/main.nf @@ -3092,9 +3092,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/bedtools/bedtools_sort", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json index 5b6710e7..1cbf84c5 100644 --- a/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json +++ b/target/nextflow/bedtools/bedtools_sort/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Output sorted file (bed/gff/vcf) to be written", "help_text": "Type: `file`, default: `$id.$key.output.output`. Output sorted file (bed/gff/vcf) to be written." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -83,7 +83,7 @@ "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" + "default":false } @@ -94,7 +94,7 @@ "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" + "default":false } @@ -105,7 +105,7 @@ "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" + "default":false } @@ -116,7 +116,7 @@ "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" + "default":false } @@ -147,7 +147,7 @@ "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" + "default":false } diff --git a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml index 5ebb52ce..a874174e 100644 --- a/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_download_datasets/.config.vsh.yaml @@ -158,9 +158,9 @@ build_info: output: "target/nextflow/busco/busco_download_datasets" executable: "target/nextflow/busco/busco_download_datasets/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/busco/busco_download_datasets/main.nf b/target/nextflow/busco/busco_download_datasets/main.nf index 04d39535..4c261314 100644 --- a/target/nextflow/busco/busco_download_datasets/main.nf +++ b/target/nextflow/busco/busco_download_datasets/main.nf @@ -3011,9 +3011,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_download_datasets", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json index 10f7d894..936911c2 100644 --- a/target/nextflow/busco/busco_download_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_download_datasets/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n", "help_text": "Type: `file`, default: `$id.$key.download_path.download_path`, example: `busco_downloads`. Local filepath for storing BUSCO dataset downloads\n" , - "default": "$id.$key.download_path.download_path" + "default":"$id.$key.download_path.download_path" } diff --git a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml index 63dc2ac3..c511dc27 100644 --- a/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml +++ b/target/nextflow/busco/busco_list_datasets/.config.vsh.yaml @@ -145,9 +145,9 @@ build_info: output: "target/nextflow/busco/busco_list_datasets" executable: "target/nextflow/busco/busco_list_datasets/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/busco/busco_list_datasets/main.nf b/target/nextflow/busco/busco_list_datasets/main.nf index 6640ad30..6694dfc6 100644 --- a/target/nextflow/busco/busco_list_datasets/main.nf +++ b/target/nextflow/busco/busco_list_datasets/main.nf @@ -2997,9 +2997,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_list_datasets", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json index c2f65754..ced3a09a 100644 --- a/target/nextflow/busco/busco_list_datasets/nextflow_schema.json +++ b/target/nextflow/busco/busco_list_datasets/nextflow_schema.json @@ -20,7 +20,7 @@ "description": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n", "help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `file.txt`. Output file of the available busco datasets\n" , - "default": "$id.$key.output.txt" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/busco/busco_run/.config.vsh.yaml b/target/nextflow/busco/busco_run/.config.vsh.yaml index 7fc2e157..52c6719b 100644 --- a/target/nextflow/busco/busco_run/.config.vsh.yaml +++ b/target/nextflow/busco/busco_run/.config.vsh.yaml @@ -423,9 +423,9 @@ build_info: output: "target/nextflow/busco/busco_run" executable: "target/nextflow/busco/busco_run/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/busco/busco_run/main.nf b/target/nextflow/busco/busco_run/main.nf index 8bdce740..df9b3f54 100644 --- a/target/nextflow/busco/busco_run/main.nf +++ b/target/nextflow/busco/busco_run/main.nf @@ -3309,9 +3309,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/busco/busco_run", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/busco/busco_run/nextflow_schema.json b/target/nextflow/busco/busco_run/nextflow_schema.json index eabf60cb..ce50aeee 100644 --- a/target/nextflow/busco/busco_run/nextflow_schema.json +++ b/target/nextflow/busco/busco_run/nextflow_schema.json @@ -62,7 +62,7 @@ "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.$key.short_summary_json.json" + "default":"$id.$key.short_summary_json.json" } @@ -73,7 +73,7 @@ "description": "Type: `file`, default: `$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.$key.short_summary_txt.txt" + "default":"$id.$key.short_summary_txt.txt" } @@ -84,7 +84,7 @@ "description": "Type: `file`, default: `$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.$key.full_table.tsv" + "default":"$id.$key.full_table.tsv" } @@ -95,7 +95,7 @@ "description": "Type: `file`, default: `$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.$key.missing_busco_list.tsv" + "default":"$id.$key.missing_busco_list.tsv" } @@ -106,7 +106,7 @@ "description": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The full output directory, if so desired", "help_text": "Type: `file`, default: `$id.$key.output_dir.output_dir`, example: `output_dir`. The full output directory, if so desired.\n" , - "default": "$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir.output_dir" } @@ -127,7 +127,7 @@ "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" + "default":false } @@ -138,7 +138,7 @@ "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" + "default":false } @@ -149,7 +149,7 @@ "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" + "default":false } @@ -160,7 +160,7 @@ "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" + "default":false } @@ -181,7 +181,7 @@ "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" + "default":false } @@ -192,7 +192,7 @@ "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" + "default":false } @@ -203,7 +203,7 @@ "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" + "default":false } @@ -234,7 +234,7 @@ "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" + "default":false } @@ -265,7 +265,7 @@ "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" + "default":false } @@ -306,7 +306,7 @@ "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" + "default":false } @@ -347,7 +347,7 @@ "description": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor", "help_text": "Type: `boolean_true`, default: `false`. Use Miniprot gene predictor.\n" , - "default": "False" + "default":false } @@ -368,7 +368,7 @@ "description": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor", "help_text": "Type: `boolean_true`, default: `false`. Use Metaeuk gene predictor.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml index 9c38bb59..582288b4 100644 --- a/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml +++ b/target/nextflow/cellranger/cellranger_mkref/.config.vsh.yaml @@ -195,9 +195,9 @@ build_info: output: "target/nextflow/cellranger/cellranger_mkref" executable: "target/nextflow/cellranger/cellranger_mkref/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/cellranger/cellranger_mkref/main.nf b/target/nextflow/cellranger/cellranger_mkref/main.nf index 21621948..50c96604 100644 --- a/target/nextflow/cellranger/cellranger_mkref/main.nf +++ b/target/nextflow/cellranger/cellranger_mkref/main.nf @@ -3059,9 +3059,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cellranger/cellranger_mkref", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json index 36aa1359..d860ac70 100644 --- a/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json +++ b/target/nextflow/cellranger/cellranger_mkref/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `cellranger_reference`. Output folder", "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `cellranger_reference`. Output folder" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/cutadapt/.config.vsh.yaml b/target/nextflow/cutadapt/.config.vsh.yaml index 39e754e8..7cbe26aa 100644 --- a/target/nextflow/cutadapt/.config.vsh.yaml +++ b/target/nextflow/cutadapt/.config.vsh.yaml @@ -740,9 +740,9 @@ build_info: output: "target/nextflow/cutadapt" executable: "target/nextflow/cutadapt/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/cutadapt/main.nf b/target/nextflow/cutadapt/main.nf index c1afb089..a7f02e16 100644 --- a/target/nextflow/cutadapt/main.nf +++ b/target/nextflow/cutadapt/main.nf @@ -3619,9 +3619,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/cutadapt", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/cutadapt/nextflow_schema.json b/target/nextflow/cutadapt/nextflow_schema.json index 09c66f90..2b7fb1b4 100644 --- a/target/nextflow/cutadapt/nextflow_schema.json +++ b/target/nextflow/cutadapt/nextflow_schema.json @@ -180,7 +180,7 @@ "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" + "default":false } @@ -203,7 +203,7 @@ "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" + "default":false } @@ -254,7 +254,7 @@ "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" + "default":false } @@ -285,7 +285,7 @@ "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" + "default":false } @@ -296,7 +296,7 @@ "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" + "default":false } @@ -319,7 +319,7 @@ "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" + "default":false } @@ -422,7 +422,7 @@ "description": "Type: `boolean_true`, default: `false`. Trim poly-A tails", "help_text": "Type: `boolean_true`, default: `false`. Trim poly-A tails" , - "default": "False" + "default":false } @@ -443,7 +443,7 @@ "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" + "default":false } @@ -504,7 +504,7 @@ "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" + "default":false } @@ -575,7 +575,7 @@ "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" + "default":false } @@ -586,7 +586,7 @@ "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" + "default":false } @@ -597,7 +597,7 @@ "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" + "default":false } @@ -630,7 +630,7 @@ "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" + "default":false } @@ -641,7 +641,7 @@ "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]" + "default":"$id.$key.output_*.fast[a,q]" } @@ -652,7 +652,7 @@ "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" + "default":false } @@ -663,7 +663,7 @@ "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" + "default":false } @@ -684,7 +684,7 @@ "description": "Type: `boolean_true`, default: `false`. Print debug information", "help_text": "Type: `boolean_true`, default: `false`. Print debug information" , - "default": "False" + "default":false } diff --git a/target/nextflow/falco/.config.vsh.yaml b/target/nextflow/falco/.config.vsh.yaml index c6e7a32b..1040200b 100644 --- a/target/nextflow/falco/.config.vsh.yaml +++ b/target/nextflow/falco/.config.vsh.yaml @@ -317,9 +317,9 @@ build_info: output: "target/nextflow/falco" executable: "target/nextflow/falco/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/falco/main.nf b/target/nextflow/falco/main.nf index ee52bf8b..25db12d1 100644 --- a/target/nextflow/falco/main.nf +++ b/target/nextflow/falco/main.nf @@ -3170,9 +3170,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/falco", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/falco/nextflow_schema.json b/target/nextflow/falco/nextflow_schema.json index b27a73a8..8d40e419 100644 --- a/target/nextflow/falco/nextflow_schema.json +++ b/target/nextflow/falco/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":false } @@ -91,7 +91,7 @@ "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" + "default":false } @@ -102,7 +102,7 @@ "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" + "default":false } @@ -123,7 +123,7 @@ "description": "Type: `file`, required, default: `$id.$key.outdir.outdir`, example: `output`. Create all output files in the specified \noutput directory", "help_text": "Type: `file`, required, default: `$id.$key.outdir.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.outdir" + "default":"$id.$key.outdir.outdir" } @@ -146,7 +146,7 @@ "description": "Type: `file`, default: `$id.$key.data_filename.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT)", "help_text": "Type: `file`, default: `$id.$key.data_filename.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.data_filename" + "default":"$id.$key.data_filename.data_filename" } @@ -157,7 +157,7 @@ "description": "Type: `file`, default: `$id.$key.report_filename.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML)", "help_text": "Type: `file`, default: `$id.$key.report_filename.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.report_filename" + "default":"$id.$key.report_filename.report_filename" } @@ -168,7 +168,7 @@ "description": "Type: `file`, default: `$id.$key.summary_filename.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT)", "help_text": "Type: `file`, default: `$id.$key.summary_filename.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.summary_filename" + "default":"$id.$key.summary_filename.summary_filename" } diff --git a/target/nextflow/fastp/.config.vsh.yaml b/target/nextflow/fastp/.config.vsh.yaml index b114c3bb..14c8381b 100644 --- a/target/nextflow/fastp/.config.vsh.yaml +++ b/target/nextflow/fastp/.config.vsh.yaml @@ -1083,9 +1083,9 @@ build_info: output: "target/nextflow/fastp" executable: "target/nextflow/fastp/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/fastp/main.nf b/target/nextflow/fastp/main.nf index 9075708e..b3df0432 100644 --- a/target/nextflow/fastp/main.nf +++ b/target/nextflow/fastp/main.nf @@ -4023,9 +4023,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastp", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/fastp/nextflow_schema.json b/target/nextflow/fastp/nextflow_schema.json index bbeb7338..bbc0c539 100644 --- a/target/nextflow/fastp/nextflow_schema.json +++ b/target/nextflow/fastp/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.out1.gz" } @@ -61,7 +61,7 @@ "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" + "default":"$id.$key.out2.gz" } @@ -72,7 +72,7 @@ "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" + "default":"$id.$key.unpaired1.gz" } @@ -83,7 +83,7 @@ "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" + "default":"$id.$key.unpaired2.gz" } @@ -94,7 +94,7 @@ "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" + "default":"$id.$key.failed_out.gz" } @@ -105,7 +105,7 @@ "description": "Type: `file`, default: `$id.$key.overlapped_out.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.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n" , - "default": "$id.$key.overlapped_out.overlapped_out" + "default":"$id.$key.overlapped_out.overlapped_out" } @@ -126,7 +126,7 @@ "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" + "default":"$id.$key.json.json" } @@ -137,7 +137,7 @@ "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" + "default":"$id.$key.html.html" } @@ -168,7 +168,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable adapter trimming", "help_text": "Type: `boolean_true`, default: `false`. Disable adapter trimming.\n" , - "default": "False" + "default":false } @@ -179,7 +179,7 @@ "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" + "default":false } @@ -300,7 +300,7 @@ "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" + "default":false } @@ -311,7 +311,7 @@ "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" + "default":"$id.$key.merged_out.gz" } @@ -322,7 +322,7 @@ "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" + "default":false } @@ -343,7 +343,7 @@ "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" + "default":false } @@ -354,7 +354,7 @@ "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" + "default":false } @@ -365,7 +365,7 @@ "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" + "default":false } @@ -396,7 +396,7 @@ "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" + "default":false } @@ -417,7 +417,7 @@ "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" + "default":false } @@ -458,7 +458,7 @@ "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" + "default":false } @@ -479,7 +479,7 @@ "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" + "default":false } @@ -500,7 +500,7 @@ "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" + "default":false } @@ -521,7 +521,7 @@ "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" + "default":false } @@ -542,7 +542,7 @@ "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" + "default":false } @@ -693,7 +693,7 @@ "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" + "default":false } @@ -754,7 +754,7 @@ "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" + "default":false } @@ -795,7 +795,7 @@ "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" + "default":false } @@ -866,7 +866,7 @@ "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" + "default":false } @@ -917,7 +917,7 @@ "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" + "default":false } @@ -990,7 +990,7 @@ "description": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis", "help_text": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 04db2265..fdd44163 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -340,9 +340,9 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 39ed05ce..221b751c 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3182,9 +3182,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/fastqc/nextflow_schema.json b/target/nextflow/fastqc/nextflow_schema.json index 75ac3990..b85804c4 100644 --- a/target/nextflow/fastqc/nextflow_schema.json +++ b/target/nextflow/fastqc/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results", "help_text": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results. \n\u0027*\u0027 wild card must be provided in the output file name. \nWild card will be replaced by the input file basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.html\"\n would create an output html file named sample_1.html\n" , - "default": "$id.$key.html_*.html" + "default":"$id.$key.html_*.html" } @@ -51,7 +51,7 @@ "description": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc", "help_text": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc.\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.zip\"\n would create an output zip file named sample_1.zip\n" , - "default": "$id.$key.zip_*.zip" + "default":"$id.$key.zip_*.zip" } @@ -62,7 +62,7 @@ "description": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s)", "help_text": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_summary.txt\"\n would create an output summary.txt file named sample_1_summary.txt\n" , - "default": "$id.$key.summary_*.txt" + "default":"$id.$key.summary_*.txt" } @@ -73,7 +73,7 @@ "description": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s)", "help_text": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_data.txt\"\n would create an output data.txt file named sample_1_data.txt\n" , - "default": "$id.$key.data_*.txt" + "default":"$id.$key.data_*.txt" } @@ -94,7 +94,7 @@ "description": "Type: `boolean_true`, default: `false`. Files come from raw casava output", "help_text": "Type: `boolean_true`, default: `false`. Files come from raw casava output. Files in the same sample\ngroup (differing only by the group number) will be analysed\nas a set rather than individually. Sequences with the filter\nflag set in the header will be excluded from the analysis.\nFiles must have the same names given to them by casava\n(including being gzipped and ending with .gz) otherwise they\nwon\u0027t be grouped together correctly.\n" , - "default": "False" + "default":false } @@ -105,7 +105,7 @@ "description": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format", "help_text": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format. In\nthis mode you can pass in directories to process and the program\nwill take in all fast5 files within those directories and produce\na single output file from the sequences found in all files.\n" , - "default": "False" + "default":false } @@ -116,7 +116,7 @@ "description": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis", "help_text": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis.\n" , - "default": "False" + "default":false } @@ -127,7 +127,7 @@ "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 the read. \nWARNING: Using this option will cause fastqc to crash \nand burn if you use it on really long reads, and your \nplots may end up a ridiculous size. You have been warned!\n" , - "default": "False" + "default":false } @@ -198,7 +198,7 @@ "description": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors", "help_text": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/featurecounts/.config.vsh.yaml b/target/nextflow/featurecounts/.config.vsh.yaml index 37865feb..f59e1f1a 100644 --- a/target/nextflow/featurecounts/.config.vsh.yaml +++ b/target/nextflow/featurecounts/.config.vsh.yaml @@ -645,9 +645,9 @@ build_info: output: "target/nextflow/featurecounts" executable: "target/nextflow/featurecounts/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/featurecounts/main.nf b/target/nextflow/featurecounts/main.nf index 6db06cc9..d9852f3d 100644 --- a/target/nextflow/featurecounts/main.nf +++ b/target/nextflow/featurecounts/main.nf @@ -3549,9 +3549,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/featurecounts", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/featurecounts/nextflow_schema.json b/target/nextflow/featurecounts/nextflow_schema.json index d55c22dd..8b277f20 100644 --- a/target/nextflow/featurecounts/nextflow_schema.json +++ b/target/nextflow/featurecounts/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.counts.tsv" } @@ -61,7 +61,7 @@ "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" + "default":"$id.$key.summary.tsv" } @@ -72,7 +72,7 @@ "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" + "default":"$id.$key.junctions.txt" } @@ -155,7 +155,7 @@ "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" + "default":false } @@ -176,7 +176,7 @@ "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" + "default":false } @@ -217,7 +217,7 @@ "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" + "default":false } @@ -290,7 +290,7 @@ "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" + "default":false } @@ -311,7 +311,7 @@ "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" + "default":false } @@ -342,7 +342,7 @@ "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" + "default":false } @@ -353,7 +353,7 @@ "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" + "default":false } @@ -364,7 +364,7 @@ "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" + "default":false } @@ -375,7 +375,7 @@ "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" + "default":false } @@ -438,7 +438,7 @@ "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" + "default":false } @@ -449,7 +449,7 @@ "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" + "default":false } @@ -460,7 +460,7 @@ "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" + "default":false } @@ -471,7 +471,7 @@ "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" + "default":false } @@ -502,7 +502,7 @@ "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" + "default":false } @@ -513,7 +513,7 @@ "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" + "default":false } @@ -534,7 +534,7 @@ "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" + "default":false } @@ -555,7 +555,7 @@ "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" + "default":false } @@ -576,7 +576,7 @@ "description": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results", "help_text": "Type: `file`, default: `$id.$key.detailed_results.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" + "default":"$id.$key.detailed_results.detailed_results" } @@ -619,7 +619,7 @@ "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" + "default":false } diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index a55dc374..d56f5cb9 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -190,9 +190,9 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index b0a41efc..ae3f2e3d 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3032,9 +3032,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/fq_subsample/nextflow_schema.json b/target/nextflow/fq_subsample/nextflow_schema.json index ace623d0..511bd91d 100644 --- a/target/nextflow/fq_subsample/nextflow_schema.json +++ b/target/nextflow/fq_subsample/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files", "help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`." , - "default": "$id.$key.output_1.output_1" + "default":"$id.$key.output_1.output_1" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files", "help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`." , - "default": "$id.$key.output_2.output_2" + "default":"$id.$key.output_2.output_2" } diff --git a/target/nextflow/gffread/.config.vsh.yaml b/target/nextflow/gffread/.config.vsh.yaml index 90eb2f2d..54dad4ba 100644 --- a/target/nextflow/gffread/.config.vsh.yaml +++ b/target/nextflow/gffread/.config.vsh.yaml @@ -685,9 +685,9 @@ build_info: output: "target/nextflow/gffread" executable: "target/nextflow/gffread/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/gffread/main.nf b/target/nextflow/gffread/main.nf index 9c3fc681..0b9416be 100644 --- a/target/nextflow/gffread/main.nf +++ b/target/nextflow/gffread/main.nf @@ -3606,9 +3606,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/gffread", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/gffread/nextflow_schema.json b/target/nextflow/gffread/nextflow_schema.json index 5d494634..5ed6b228 100644 --- a/target/nextflow/gffread/nextflow_schema.json +++ b/target/nextflow/gffread/nextflow_schema.json @@ -70,7 +70,7 @@ "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" + "default":"$id.$key.outfile.gff" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -92,7 +92,7 @@ "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" + "default":false } @@ -103,7 +103,7 @@ "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" + "default":false } @@ -114,7 +114,7 @@ "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" + "default":false } @@ -125,7 +125,7 @@ "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" + "default":false } @@ -136,7 +136,7 @@ "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" + "default":false } @@ -147,7 +147,7 @@ "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" + "default":"$id.$key.spliced_exons.fa" } @@ -168,7 +168,7 @@ "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" + "default":false } @@ -199,7 +199,7 @@ "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" + "default":false } @@ -210,7 +210,7 @@ "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" + "default":false } @@ -221,7 +221,7 @@ "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" + "default":false } @@ -242,7 +242,7 @@ "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" + "default":false } @@ -253,7 +253,7 @@ "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" + "default":false } @@ -264,7 +264,7 @@ "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" + "default":false } @@ -285,7 +285,7 @@ "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" + "default":false } @@ -356,7 +356,7 @@ "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" + "default":false } @@ -377,7 +377,7 @@ "description": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts", "help_text": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts.\n" , - "default": "False" + "default":false } @@ -388,7 +388,7 @@ "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" + "default":false } @@ -399,7 +399,7 @@ "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" + "default":false } @@ -410,7 +410,7 @@ "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" + "default":false } @@ -421,7 +421,7 @@ "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" + "default":false } @@ -442,7 +442,7 @@ "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" + "default":false } @@ -473,7 +473,7 @@ "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" + "default":false } @@ -484,7 +484,7 @@ "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" + "default":false } @@ -495,7 +495,7 @@ "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" + "default":false } @@ -516,7 +516,7 @@ "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" + "default":false } @@ -527,7 +527,7 @@ "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" + "default":false } @@ -538,7 +538,7 @@ "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" + "default":false } @@ -549,7 +549,7 @@ "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" + "default":false } @@ -560,7 +560,7 @@ "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" + "default":false } @@ -571,7 +571,7 @@ "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" + "default":false } @@ -582,7 +582,7 @@ "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" + "default":false } @@ -593,7 +593,7 @@ "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" + "default":false } @@ -604,7 +604,7 @@ "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" + "default":false } @@ -615,7 +615,7 @@ "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" + "default":false } @@ -626,7 +626,7 @@ "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" + "default":false } @@ -637,7 +637,7 @@ "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" + "default":false } @@ -648,7 +648,7 @@ "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" + "default":false } @@ -659,7 +659,7 @@ "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" + "default":false } @@ -670,7 +670,7 @@ "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" + "default":false } @@ -691,7 +691,7 @@ "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" + "default":false } @@ -712,7 +712,7 @@ "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" + "default":false } @@ -723,7 +723,7 @@ "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" + "default":false } @@ -734,7 +734,7 @@ "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" + "default":false } @@ -745,7 +745,7 @@ "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" + "default":false } diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 659174a4..adb39ffd 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -218,9 +218,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index fa3ac853..c324d4a8 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3071,9 +3071,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json index bf4b2c8a..6d0b6164 100644 --- a/target/nextflow/kallisto/kallisto_index/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_index/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. ", "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. " , - "default": "$id.$key.index.index" + "default":"$id.$key.index.index" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -92,7 +92,7 @@ "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" + "default":false } @@ -103,7 +103,7 @@ "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" + "default":false } diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index db6bb9a0..75ae5e74 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -246,9 +246,9 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index bec853b8..d8f9d467 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3105,9 +3105,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json index 260d9ca6..40a2444f 100644 --- a/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json +++ b/target/nextflow/kallisto/kallisto_quant/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to", "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to." , - "default": "$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir.output_dir" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant", "help_text": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant" , - "default": "$id.$key.log.log" + "default":"$id.$key.log.log" } @@ -82,7 +82,7 @@ "description": "Type: `boolean_true`, default: `false`. Single end mode", "help_text": "Type: `boolean_true`, default: `false`. Single end mode." , - "default": "False" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -115,7 +115,7 @@ "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" + "default":false } @@ -146,7 +146,7 @@ "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" + "default":false } diff --git a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml index 3d791fd2..b87e1f30 100644 --- a/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_call/.config.vsh.yaml @@ -507,9 +507,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_call" executable: "target/nextflow/lofreq/lofreq_call/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/lofreq/lofreq_call/main.nf b/target/nextflow/lofreq/lofreq_call/main.nf index 49785fb6..ec74457f 100644 --- a/target/nextflow/lofreq/lofreq_call/main.nf +++ b/target/nextflow/lofreq/lofreq_call/main.nf @@ -3414,9 +3414,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_call", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/lofreq/lofreq_call/nextflow_schema.json b/target/nextflow/lofreq/lofreq_call/nextflow_schema.json index 431e363e..da924c4f 100644 --- a/target/nextflow/lofreq/lofreq_call/nextflow_schema.json +++ b/target/nextflow/lofreq/lofreq_call/nextflow_schema.json @@ -60,7 +60,7 @@ "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" + "default":"$id.$key.out.vcf" } @@ -161,7 +161,7 @@ "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" + "default":false } @@ -172,7 +172,7 @@ "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" + "default":false } @@ -183,7 +183,7 @@ "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" + "default":false } @@ -194,7 +194,7 @@ "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" + "default":false } @@ -225,7 +225,7 @@ "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" + "default":false } @@ -236,7 +236,7 @@ "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" + "default":false } @@ -247,7 +247,7 @@ "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" + "default":false } @@ -258,7 +258,7 @@ "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" + "default":false } @@ -329,7 +329,7 @@ "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" + "default":false } @@ -340,7 +340,7 @@ "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" + "default":false } @@ -351,7 +351,7 @@ "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" + "default":false } @@ -362,7 +362,7 @@ "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" + "default":false } @@ -373,7 +373,7 @@ "description": "Type: `boolean_true`, default: `false`. Overwrite any existing output", "help_text": "Type: `boolean_true`, default: `false`. Overwrite any existing output.\n" , - "default": "False" + "default":false } @@ -384,7 +384,7 @@ "description": "Type: `boolean_true`, default: `false`. Be verbose", "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n" , - "default": "False" + "default":false } @@ -395,7 +395,7 @@ "description": "Type: `boolean_true`, default: `false`. Enable debugging", "help_text": "Type: `boolean_true`, default: `false`. Enable debugging.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml index 699c5f42..c7b51039 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml +++ b/target/nextflow/lofreq/lofreq_indelqual/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/nextflow/lofreq/lofreq_indelqual" executable: "target/nextflow/lofreq/lofreq_indelqual/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/lofreq/lofreq_indelqual/main.nf b/target/nextflow/lofreq/lofreq_indelqual/main.nf index 4fa22b70..9a41f985 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/main.nf +++ b/target/nextflow/lofreq/lofreq_indelqual/main.nf @@ -3077,9 +3077,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/lofreq/lofreq_indelqual", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json index fc09ea50..2ee7baf6 100644 --- a/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json +++ b/target/nextflow/lofreq/lofreq_indelqual/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.out.bam" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -92,7 +92,7 @@ "description": "Type: `boolean_true`, default: `false`. Be verbose", "help_text": "Type: `boolean_true`, default: `false`. Be verbose.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/multiqc/.config.vsh.yaml b/target/nextflow/multiqc/.config.vsh.yaml index eddcbaee..3475e44c 100644 --- a/target/nextflow/multiqc/.config.vsh.yaml +++ b/target/nextflow/multiqc/.config.vsh.yaml @@ -456,9 +456,9 @@ build_info: output: "target/nextflow/multiqc" executable: "target/nextflow/multiqc/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/multiqc/main.nf b/target/nextflow/multiqc/main.nf index 9abc618a..71ef4c3a 100644 --- a/target/nextflow/multiqc/main.nf +++ b/target/nextflow/multiqc/main.nf @@ -3366,9 +3366,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/multiqc", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/multiqc/nextflow_schema.json b/target/nextflow/multiqc/nextflow_schema.json index 5f3f25eb..6a3bd5c6 100644 --- a/target/nextflow/multiqc/nextflow_schema.json +++ b/target/nextflow/multiqc/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output_report.html" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files", "help_text": "Type: `file`, default: `$id.$key.output_data.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_data" + "default":"$id.$key.output_data.output_data" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots", "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n" , - "default": "$id.$key.output_plots.output_plots" + "default":"$id.$key.output_plots.output_plots" } @@ -123,7 +123,7 @@ "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" + "default":false } @@ -144,7 +144,7 @@ "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" + "default":false } @@ -165,7 +165,7 @@ "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" + "default":false } @@ -176,7 +176,7 @@ "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" + "default":false } @@ -269,7 +269,7 @@ "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" + "default":false } @@ -290,7 +290,7 @@ "description": "Type: `boolean_true`, default: `false`. Increase output verbosity", "help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n" , - "default": "False" + "default":false } @@ -301,7 +301,7 @@ "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" + "default":false } @@ -312,7 +312,7 @@ "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" + "default":false } @@ -323,7 +323,7 @@ "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" + "default":false } @@ -334,7 +334,7 @@ "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" + "default":false } @@ -345,7 +345,7 @@ "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" + "default":false } @@ -356,7 +356,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable coloured log output", "help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n" , - "default": "False" + "default":false } @@ -387,7 +387,7 @@ "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" + "default":false } @@ -398,7 +398,7 @@ "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" + "default":false } @@ -409,7 +409,7 @@ "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" + "default":false } @@ -420,7 +420,7 @@ "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" + "default":false } @@ -431,7 +431,7 @@ "description": "Type: `boolean_true`, default: `false`. Compress the data directory", "help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n" , - "default": "False" + "default":false } @@ -454,7 +454,7 @@ "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" + "default":false } diff --git a/target/nextflow/nanoplot/.config.vsh.yaml b/target/nextflow/nanoplot/.config.vsh.yaml index 9a8ff624..6cdbe1f9 100644 --- a/target/nextflow/nanoplot/.config.vsh.yaml +++ b/target/nextflow/nanoplot/.config.vsh.yaml @@ -492,9 +492,9 @@ build_info: output: "target/nextflow/nanoplot" executable: "target/nextflow/nanoplot/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/nanoplot/main.nf b/target/nextflow/nanoplot/main.nf index 0ca0b999..844558f1 100644 --- a/target/nextflow/nanoplot/main.nf +++ b/target/nextflow/nanoplot/main.nf @@ -3397,9 +3397,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/nanoplot", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/nanoplot/nextflow_schema.json b/target/nextflow/nanoplot/nextflow_schema.json index d778e7a0..81c5d459 100644 --- a/target/nextflow/nanoplot/nextflow_schema.json +++ b/target/nextflow/nanoplot/nextflow_schema.json @@ -130,7 +130,7 @@ "description": "Type: `file`, required, default: `$id.$key.outdir.outdir`. Specify directory in which output has to be created", "help_text": "Type: `file`, required, default: `$id.$key.outdir.outdir`. Specify directory in which output has to be created." , - "default": "$id.$key.outdir.outdir" + "default":"$id.$key.outdir.outdir" } @@ -151,7 +151,7 @@ "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" + "default":false } @@ -162,7 +162,7 @@ "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" + "default":false } @@ -173,7 +173,7 @@ "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" + "default":false } @@ -184,7 +184,7 @@ "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" + "default":false } @@ -195,7 +195,7 @@ "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" + "default":true } @@ -216,7 +216,7 @@ "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" + "default":false } @@ -227,7 +227,7 @@ "description": "Type: `boolean_true`, default: `false`. Output only the report", "help_text": "Type: `boolean_true`, default: `false`. Output only the report." , - "default": "False" + "default":false } @@ -238,7 +238,7 @@ "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" + "default":false } @@ -279,7 +279,7 @@ "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" + "default":true } @@ -300,7 +300,7 @@ "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" + "default":false } @@ -311,7 +311,7 @@ "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" + "default":false } @@ -322,7 +322,7 @@ "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" + "default":false } @@ -363,7 +363,7 @@ "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" + "default":false } @@ -374,7 +374,7 @@ "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" + "default":true } @@ -415,7 +415,7 @@ "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" + "default":"png" } @@ -446,7 +446,7 @@ "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" + "default":false } @@ -457,7 +457,7 @@ "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" + "default":false } @@ -468,7 +468,7 @@ "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" + "default":true } @@ -479,7 +479,7 @@ "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" + "default":false } @@ -520,7 +520,7 @@ "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" + "default":true } diff --git a/target/nextflow/pear/.config.vsh.yaml b/target/nextflow/pear/.config.vsh.yaml index 78ee96bd..0eaa52da 100644 --- a/target/nextflow/pear/.config.vsh.yaml +++ b/target/nextflow/pear/.config.vsh.yaml @@ -398,9 +398,9 @@ build_info: output: "target/nextflow/pear" executable: "target/nextflow/pear/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/pear/main.nf b/target/nextflow/pear/main.nf index a56f51fc..9a7f180f 100644 --- a/target/nextflow/pear/main.nf +++ b/target/nextflow/pear/main.nf @@ -3259,9 +3259,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/pear", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/pear/nextflow_schema.json b/target/nextflow/pear/nextflow_schema.json index 77dee5c8..af164e71 100644 --- a/target/nextflow/pear/nextflow_schema.json +++ b/target/nextflow/pear/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.assembled.assembled`. The output file containing assembled reads", "help_text": "Type: `file`, required, default: `$id.$key.assembled.assembled`. The output file containing assembled reads. Can be compressed with gzip." , - "default": "$id.$key.assembled.assembled" + "default":"$id.$key.assembled.assembled" } @@ -61,7 +61,7 @@ "description": "Type: `file`, required, default: `$id.$key.unassembled_forward.unassembled_forward`. The output file containing forward reads that could not be assembled", "help_text": "Type: `file`, required, default: `$id.$key.unassembled_forward.unassembled_forward`. The output file containing forward reads that could not be assembled. Can be compressed with gzip." , - "default": "$id.$key.unassembled_forward.unassembled_forward" + "default":"$id.$key.unassembled_forward.unassembled_forward" } @@ -72,7 +72,7 @@ "description": "Type: `file`, required, default: `$id.$key.unassembled_reverse.unassembled_reverse`. The output file containing reverse reads that could not be assembled", "help_text": "Type: `file`, required, default: `$id.$key.unassembled_reverse.unassembled_reverse`. The output file containing reverse reads that could not be assembled. Can be compressed with gzip." , - "default": "$id.$key.unassembled_reverse.unassembled_reverse" + "default":"$id.$key.unassembled_reverse.unassembled_reverse" } @@ -83,7 +83,7 @@ "description": "Type: `file`, required, default: `$id.$key.discarded.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.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.discarded" + "default":"$id.$key.discarded.discarded" } @@ -184,7 +184,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable empirical base frequencies", "help_text": "Type: `boolean_true`, default: `false`. Disable empirical base frequencies.\n" , - "default": "False" + "default":false } @@ -225,7 +225,7 @@ "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" + "default":false } diff --git a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml index 4a1b9adc..b4b05536 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml +++ b/target/nextflow/qualimap/qualimap_rnaseq/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/nextflow/qualimap/qualimap_rnaseq" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/qualimap/qualimap_rnaseq/main.nf b/target/nextflow/qualimap/qualimap_rnaseq/main.nf index 0d70bedd..5acb4baa 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/main.nf +++ b/target/nextflow/qualimap/qualimap_rnaseq/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/qualimap/qualimap_rnaseq", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json index aaf2e054..37135d51 100644 --- a/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json +++ b/target/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.qc_results.txt" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts", "help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts." , - "default": "$id.$key.counts.counts" + "default":"$id.$key.counts.counts" } @@ -72,7 +72,7 @@ "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" + "default":"$id.$key.report.html" } @@ -137,7 +137,7 @@ "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" + "default":false } @@ -148,7 +148,7 @@ "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" + "default":false } diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 780fa6de..4e942c80 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -852,9 +852,9 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 79614063..56e7d179 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3661,9 +3661,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json index c0aedaec..63db46df 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json @@ -42,7 +42,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":"$id.$key.counts_gene.results" } @@ -104,7 +104,7 @@ "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" + "default":"$id.$key.counts_transcripts.results" } @@ -115,7 +115,7 @@ "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" + "default":"$id.$key.stat.stat" } @@ -126,7 +126,7 @@ "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" + "default":"$id.$key.logs.log" } @@ -137,7 +137,7 @@ "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" + "default":"$id.$key.bam_star.bam" } @@ -148,7 +148,7 @@ "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" + "default":"$id.$key.bam_genome.bam" } @@ -159,7 +159,7 @@ "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" + "default":"$id.$key.bam_transcript.bam" } @@ -170,7 +170,7 @@ "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" + "default":false } @@ -181,7 +181,7 @@ "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" + "default":false } @@ -192,7 +192,7 @@ "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" + "default":false } @@ -203,7 +203,7 @@ "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" + "default":false } @@ -214,7 +214,7 @@ "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" + "default":false } @@ -235,7 +235,7 @@ "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" + "default":false } @@ -246,7 +246,7 @@ "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" + "default":false } @@ -267,7 +267,7 @@ "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" + "default":false } @@ -278,7 +278,7 @@ "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" + "default":false } @@ -289,7 +289,7 @@ "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" + "default":false } @@ -300,7 +300,7 @@ "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" + "default":false } @@ -321,7 +321,7 @@ "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" + "default":false } @@ -332,7 +332,7 @@ "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" + "default":false } @@ -343,7 +343,7 @@ "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" + "default":false } @@ -354,7 +354,7 @@ "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" + "default":false } @@ -385,7 +385,7 @@ "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" + "default":false } @@ -396,7 +396,7 @@ "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" + "default":false } @@ -481,7 +481,7 @@ "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" + "default":false } @@ -492,7 +492,7 @@ "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" + "default":false } @@ -503,7 +503,7 @@ "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" + "default":false } @@ -574,7 +574,7 @@ "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" + "default":false } @@ -645,7 +645,7 @@ "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" + "default":false } @@ -666,7 +666,7 @@ "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" + "default":false } @@ -687,7 +687,7 @@ "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" + "default":false } @@ -748,7 +748,7 @@ "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" + "default":false } diff --git a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml index b77ed360..94266b8a 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml @@ -416,9 +416,9 @@ build_info: output: "target/nextflow/rsem/rsem_prepare_reference" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/rsem/rsem_prepare_reference/main.nf b/target/nextflow/rsem/rsem_prepare_reference/main.nf index 01da6805..e4f08ad0 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/main.nf +++ b/target/nextflow/rsem/rsem_prepare_reference/main.nf @@ -3245,9 +3245,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rsem/rsem_prepare_reference", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json index 14742746..1a04a5e7 100644 --- a/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json +++ b/target/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -101,7 +101,7 @@ "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" + "default":false } @@ -142,7 +142,7 @@ "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" + "default":false } @@ -173,7 +173,7 @@ "description": "Type: `boolean_true`, default: `false`. Build Bowtie indices", "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie indices." , - "default": "False" + "default":false } @@ -184,7 +184,7 @@ "description": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices", "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices." , - "default": "False" + "default":false } @@ -195,7 +195,7 @@ "description": "Type: `boolean_true`, default: `false`. Build STAR indices", "help_text": "Type: `boolean_true`, default: `false`. Build STAR indices." , - "default": "False" + "default":false } @@ -216,7 +216,7 @@ "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" + "default":false } @@ -227,7 +227,7 @@ "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" + "default":false } @@ -248,7 +248,7 @@ "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" + "default":false } diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 1bd8d27e..a1eb2e26 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -175,9 +175,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index e64063b2..043175f4 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3036,9 +3036,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json index 21b1df1b..e84def6b 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics", "help_text": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 73ab053b..dd249054 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -201,9 +201,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 1a007adc..8c96bf65 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3069,9 +3069,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json index 5ac5937d..1ab703cb 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml index ccf4c4a7..43639d09 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inner_distance/.config.vsh.yaml @@ -294,9 +294,9 @@ build_info: output: "target/nextflow/rseqc/rseqc_inner_distance" executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/rseqc/rseqc_inner_distance/main.nf b/target/nextflow/rseqc/rseqc_inner_distance/main.nf index de086a14..0a0e0ec0 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/main.nf +++ b/target/nextflow/rseqc/rseqc_inner_distance/main.nf @@ -3169,9 +3169,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/rseqc/rseqc_inner_distance", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json index 34e93183..9f62271a 100644 --- a/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json +++ b/target/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json @@ -110,7 +110,7 @@ "description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads", "help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads" , - "default": "$id.$key.output_stats.output_stats" + "default":"$id.$key.output_stats.output_stats" } @@ -121,7 +121,7 @@ "description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads" , - "default": "$id.$key.output_dist.output_dist" + "default":"$id.$key.output_dist.output_dist" } @@ -132,7 +132,7 @@ "description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads", "help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads" , - "default": "$id.$key.output_freq.output_freq" + "default":"$id.$key.output_freq.output_freq" } @@ -143,7 +143,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot.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_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.output_plot.output_plot" + "default":"$id.$key.output_plot.output_plot" } @@ -154,7 +154,7 @@ "description": "Type: `file`, default: `$id.$key.output_plot_r.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_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads" , - "default": "$id.$key.output_plot_r.output_plot_r" + "default":"$id.$key.output_plot_r.output_plot_r" } diff --git a/target/nextflow/salmon/salmon_index/.config.vsh.yaml b/target/nextflow/salmon/salmon_index/.config.vsh.yaml index 9426bd8b..29e1d6a5 100644 --- a/target/nextflow/salmon/salmon_index/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_index/.config.vsh.yaml @@ -277,9 +277,9 @@ build_info: output: "target/nextflow/salmon/salmon_index" executable: "target/nextflow/salmon/salmon_index/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/salmon/salmon_index/main.nf b/target/nextflow/salmon/salmon_index/main.nf index 66caf723..33a48b3a 100644 --- a/target/nextflow/salmon/salmon_index/main.nf +++ b/target/nextflow/salmon/salmon_index/main.nf @@ -3129,9 +3129,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_index", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/salmon/salmon_index/nextflow_schema.json b/target/nextflow/salmon/salmon_index/nextflow_schema.json index 9c282208..d21c0eee 100644 --- a/target/nextflow/salmon/salmon_index/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_index/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":false } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -83,7 +83,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -125,7 +125,7 @@ "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" + "default":false } @@ -156,7 +156,7 @@ "description": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n", "help_text": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n" , - "default": "$id.$key.index.index" + "default":"$id.$key.index.index" } diff --git a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml index 1f7058ac..cdcde821 100644 --- a/target/nextflow/salmon/salmon_quant/.config.vsh.yaml +++ b/target/nextflow/salmon/salmon_quant/.config.vsh.yaml @@ -1173,9 +1173,9 @@ build_info: output: "target/nextflow/salmon/salmon_quant" executable: "target/nextflow/salmon/salmon_quant/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/salmon/salmon_quant/main.nf b/target/nextflow/salmon/salmon_quant/main.nf index 21999e3a..c86bbd59 100644 --- a/target/nextflow/salmon/salmon_quant/main.nf +++ b/target/nextflow/salmon/salmon_quant/main.nf @@ -3964,9 +3964,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/salmon/salmon_quant", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/salmon/salmon_quant/nextflow_schema.json b/target/nextflow/salmon/salmon_quant/nextflow_schema.json index 0b9e23d9..16d210f5 100644 --- a/target/nextflow/salmon/salmon_quant/nextflow_schema.json +++ b/target/nextflow/salmon/salmon_quant/nextflow_schema.json @@ -22,7 +22,7 @@ "enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"] , - "default": "A" + "default":"A" } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -134,7 +134,7 @@ "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" + "default":false } @@ -155,7 +155,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory", "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -166,7 +166,7 @@ "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" + "default":"$id.$key.quant_results.sf" } @@ -187,7 +187,7 @@ "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" + "default":false } @@ -198,7 +198,7 @@ "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" + "default":false } @@ -209,7 +209,7 @@ "description": "Type: `boolean_true`, default: `false`. Perform positional bias correction", "help_text": "Type: `boolean_true`, default: `false`. Perform positional bias correction.\n" , - "default": "False" + "default":false } @@ -250,7 +250,7 @@ "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" + "default":false } @@ -281,7 +281,7 @@ "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" + "default":false } @@ -352,7 +352,7 @@ "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" + "default":false } @@ -423,7 +423,7 @@ "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" + "default":false } @@ -434,7 +434,7 @@ "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" + "default":false } @@ -445,7 +445,7 @@ "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" + "default":false } @@ -456,7 +456,7 @@ "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" + "default":false } @@ -467,7 +467,7 @@ "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" + "default":false } @@ -478,7 +478,7 @@ "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" + "default":false } @@ -489,7 +489,7 @@ "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" + "default":false } @@ -500,7 +500,7 @@ "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" + "default":false } @@ -521,7 +521,7 @@ "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" + "default":false } @@ -532,7 +532,7 @@ "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" + "default":"$id.$key.mapping_sam.sam" } @@ -543,7 +543,7 @@ "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" + "default":false } @@ -576,7 +576,7 @@ "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" + "default":false } @@ -587,7 +587,7 @@ "description": "Type: `file`, default: `$id.$key.aux_dir.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.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.aux_dir" + "default":"$id.$key.aux_dir.aux_dir" } @@ -598,7 +598,7 @@ "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" + "default":false } @@ -609,7 +609,7 @@ "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" + "default":false } @@ -620,7 +620,7 @@ "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" + "default":false } @@ -641,7 +641,7 @@ "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" + "default":false } @@ -702,7 +702,7 @@ "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" + "default":false } @@ -733,7 +733,7 @@ "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" + "default":false } @@ -744,7 +744,7 @@ "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" + "default":false } @@ -755,7 +755,7 @@ "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" + "default":false } @@ -766,7 +766,7 @@ "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" + "default":false } @@ -777,7 +777,7 @@ "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" + "default":false } @@ -818,7 +818,7 @@ "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" + "default":false } @@ -829,7 +829,7 @@ "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" + "default":false } @@ -860,7 +860,7 @@ "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" + "default":false } @@ -881,7 +881,7 @@ "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" + "default":false } @@ -902,7 +902,7 @@ "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" + "default":false } @@ -913,7 +913,7 @@ "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" + "default":false } @@ -924,7 +924,7 @@ "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" + "default":false } @@ -955,7 +955,7 @@ "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" + "default":false } @@ -966,7 +966,7 @@ "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" + "default":false } @@ -987,7 +987,7 @@ "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" + "default":false } @@ -1008,7 +1008,7 @@ "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" + "default":false } @@ -1019,7 +1019,7 @@ "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" + "default":false } @@ -1030,7 +1030,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml index d6309c9d..dd352fbd 100644 --- a/target/nextflow/samtools/samtools_collate/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_collate/.config.vsh.yaml @@ -264,9 +264,9 @@ build_info: output: "target/nextflow/samtools/samtools_collate" executable: "target/nextflow/samtools/samtools_collate/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_collate/main.nf b/target/nextflow/samtools/samtools_collate/main.nf index 080c1c6f..cd738bce 100644 --- a/target/nextflow/samtools/samtools_collate/main.nf +++ b/target/nextflow/samtools/samtools_collate/main.nf @@ -3140,9 +3140,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_collate", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_collate/nextflow_schema.json b/target/nextflow/samtools/samtools_collate/nextflow_schema.json index 677a7322..dc33ceb5 100644 --- a/target/nextflow/samtools/samtools_collate/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_collate/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. The output filename", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. The output filename." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -71,7 +71,7 @@ "description": "Type: `boolean_true`, default: `false`. Output uncompressed BAM", "help_text": "Type: `boolean_true`, default: `false`. Output uncompressed BAM." , - "default": "False" + "default":false } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":10000 } @@ -104,7 +104,7 @@ "description": "Type: `integer`, default: `1`. Compression level", "help_text": "Type: `integer`, default: `1`. Compression level." , - "default": "1" + "default":1 } @@ -115,7 +115,7 @@ "description": "Type: `integer`, default: `64`. Number of temporary files", "help_text": "Type: `integer`, default: `64`. Number of temporary files." , - "default": "64" + "default":64 } @@ -136,7 +136,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml index d9c36d1b..028cf6e8 100644 --- a/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_faidx/.config.vsh.yaml @@ -243,9 +243,9 @@ build_info: output: "target/nextflow/samtools/samtools_faidx" executable: "target/nextflow/samtools/samtools_faidx/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_faidx/main.nf b/target/nextflow/samtools/samtools_faidx/main.nf index af69c7b9..2cb06f78 100644 --- a/target/nextflow/samtools/samtools_faidx/main.nf +++ b/target/nextflow/samtools/samtools_faidx/main.nf @@ -3112,9 +3112,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_faidx", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_faidx/nextflow_schema.json b/target/nextflow/samtools/samtools_faidx/nextflow_schema.json index 5e00f832..393a3f97 100644 --- a/target/nextflow/samtools/samtools_faidx/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_faidx/nextflow_schema.json @@ -30,7 +30,7 @@ "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" + "default":60 } @@ -61,7 +61,7 @@ "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" + "default":"$id.$key.output.fasta" } @@ -72,7 +72,7 @@ "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" + "default":"rc" } @@ -83,7 +83,7 @@ "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" + "default":"$id.$key.fai_idx.fai" } @@ -94,7 +94,7 @@ "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" + "default":"$id.$key.gzi_idx.gzi" } @@ -105,7 +105,7 @@ "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" + "default":false } @@ -126,7 +126,7 @@ "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" + "default":false } @@ -137,7 +137,7 @@ "description": "Type: `boolean_true`, default: `false`. Reverse complement sequences", "help_text": "Type: `boolean_true`, default: `false`. Reverse complement sequences.\n" , - "default": "False" + "default":false } diff --git a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml index 0419e17e..4cbd67fd 100644 --- a/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fasta/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/nextflow/samtools/samtools_fasta" executable: "target/nextflow/samtools/samtools_fasta/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_fasta/main.nf b/target/nextflow/samtools/samtools_fasta/main.nf index bf37f80b..ff2f5523 100644 --- a/target/nextflow/samtools/samtools_fasta/main.nf +++ b/target/nextflow/samtools/samtools_fasta/main.nf @@ -3304,9 +3304,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fasta", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json index 730fe87a..0d14b9b7 100644 --- a/target/nextflow/samtools/samtools_fasta/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fasta/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTA file" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -83,7 +83,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -125,7 +125,7 @@ "description": "Type: `file`, default: `$id.$key.read1.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.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.read1" + "default":"$id.$key.read1.read1" } @@ -136,7 +136,7 @@ "description": "Type: `file`, default: `$id.$key.read2.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.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.read2" + "default":"$id.$key.read2.read2" } @@ -147,7 +147,7 @@ "description": "Type: `file`, default: `$id.$key.output_reads.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.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" + "default":"$id.$key.output_reads.output_reads" } @@ -158,7 +158,7 @@ "description": "Type: `file`, default: `$id.$key.output_reads_both.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.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.output_reads_both" + "default":"$id.$key.output_reads_both.output_reads_both" } @@ -229,7 +229,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml index 1c118220..8dd1bf85 100644 --- a/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_fastq/.config.vsh.yaml @@ -433,9 +433,9 @@ build_info: output: "target/nextflow/samtools/samtools_fastq" executable: "target/nextflow/samtools/samtools_fastq/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_fastq/main.nf b/target/nextflow/samtools/samtools_fastq/main.nf index 41110337..03d73ad1 100644 --- a/target/nextflow/samtools/samtools_fastq/main.nf +++ b/target/nextflow/samtools/samtools_fastq/main.nf @@ -3304,9 +3304,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_fastq", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json index ecbf2b28..b1bdb1a1 100644 --- a/target/nextflow/samtools/samtools_fastq/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_fastq/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. output FASTQ file" , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -83,7 +83,7 @@ "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" + "default":false } @@ -104,7 +104,7 @@ "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" + "default":false } @@ -125,7 +125,7 @@ "description": "Type: `file`, default: `$id.$key.read1.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.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.read1" + "default":"$id.$key.read1.read1" } @@ -136,7 +136,7 @@ "description": "Type: `file`, default: `$id.$key.read2.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.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.read2" + "default":"$id.$key.read2.read2" } @@ -147,7 +147,7 @@ "description": "Type: `file`, default: `$id.$key.output_reads.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.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" + "default":"$id.$key.output_reads.output_reads" } @@ -158,7 +158,7 @@ "description": "Type: `file`, default: `$id.$key.output_reads_both.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.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.output_reads_both" + "default":"$id.$key.output_reads_both.output_reads_both" } @@ -229,7 +229,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml index 4efc0e0e..16adec46 100644 --- a/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_flagstat/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/samtools/samtools_flagstat" executable: "target/nextflow/samtools/samtools_flagstat/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_flagstat/main.nf b/target/nextflow/samtools/samtools_flagstat/main.nf index b6371670..31df84f1 100644 --- a/target/nextflow/samtools/samtools_flagstat/main.nf +++ b/target/nextflow/samtools/samtools_flagstat/main.nf @@ -3028,9 +3028,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_flagstat", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json b/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json index 6c3cfd06..77d8de7e 100644 --- a/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_flagstat/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.output.flagstat" } diff --git a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml index 5bc8c434..ef273e92 100644 --- a/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_idxstats/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/nextflow/samtools/samtools_idxstats" executable: "target/nextflow/samtools/samtools_idxstats/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_idxstats/main.nf b/target/nextflow/samtools/samtools_idxstats/main.nf index 86aa0a27..2729e99b 100644 --- a/target/nextflow/samtools/samtools_idxstats/main.nf +++ b/target/nextflow/samtools/samtools_idxstats/main.nf @@ -3040,9 +3040,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_idxstats", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json b/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json index 8426544a..3b43ccc8 100644 --- a/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_idxstats/nextflow_schema.json @@ -60,7 +60,7 @@ "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" + "default":"$id.$key.output.idxstats" } diff --git a/target/nextflow/samtools/samtools_index/.config.vsh.yaml b/target/nextflow/samtools/samtools_index/.config.vsh.yaml index 7c6beaa4..a4ffaa2e 100644 --- a/target/nextflow/samtools/samtools_index/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_index/.config.vsh.yaml @@ -189,9 +189,9 @@ build_info: output: "target/nextflow/samtools/samtools_index" executable: "target/nextflow/samtools/samtools_index/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_index/main.nf b/target/nextflow/samtools/samtools_index/main.nf index 210ff4b2..85b710da 100644 --- a/target/nextflow/samtools/samtools_index/main.nf +++ b/target/nextflow/samtools/samtools_index/main.nf @@ -3053,9 +3053,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_index", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_index/nextflow_schema.json b/target/nextflow/samtools/samtools_index/nextflow_schema.json index 38b24926..1617235c 100644 --- a/target/nextflow/samtools/samtools_index/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_index/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.bai" } @@ -61,7 +61,7 @@ "description": "Type: `boolean_true`, default: `false`. Generate BAM index", "help_text": "Type: `boolean_true`, default: `false`. Generate BAM index" , - "default": "False" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml index 4933b68a..d341c2f9 100644 --- a/target/nextflow/samtools/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_sort/.config.vsh.yaml @@ -332,9 +332,9 @@ build_info: output: "target/nextflow/samtools/samtools_sort" executable: "target/nextflow/samtools/samtools_sort/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_sort/main.nf b/target/nextflow/samtools/samtools_sort/main.nf index b48f412a..81aa788c 100644 --- a/target/nextflow/samtools/samtools_sort/main.nf +++ b/target/nextflow/samtools/samtools_sort/main.nf @@ -3225,9 +3225,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_sort", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_sort/nextflow_schema.json b/target/nextflow/samtools/samtools_sort/nextflow_schema.json index 74147b33..b46fa994 100644 --- a/target/nextflow/samtools/samtools_sort/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_sort/nextflow_schema.json @@ -40,7 +40,7 @@ "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" + "default":"$id.$key.output.bam" } @@ -81,7 +81,7 @@ "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" + "default":false } @@ -102,7 +102,7 @@ "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" + "default":false } @@ -113,7 +113,7 @@ "description": "Type: `boolean_true`, default: `false`. Sort by template-coordinate", "help_text": "Type: `boolean_true`, default: `false`. Sort by template-coordinate.\n" , - "default": "False" + "default":false } @@ -144,7 +144,7 @@ "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" + "default":0 } @@ -155,7 +155,7 @@ "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" + "default":false } @@ -166,7 +166,7 @@ "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" + "default":false } @@ -177,7 +177,7 @@ "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" + "default":false } @@ -218,7 +218,7 @@ "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" + "default":false } @@ -229,7 +229,7 @@ "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" + "default":false } @@ -240,7 +240,7 @@ "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" + "default":false } diff --git a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml index 90ed44aa..208326ce 100644 --- a/target/nextflow/samtools/samtools_stats/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_stats/.config.vsh.yaml @@ -401,9 +401,9 @@ build_info: output: "target/nextflow/samtools/samtools_stats" executable: "target/nextflow/samtools/samtools_stats/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_stats/main.nf b/target/nextflow/samtools/samtools_stats/main.nf index 4faeaa18..958eac0c 100644 --- a/target/nextflow/samtools/samtools_stats/main.nf +++ b/target/nextflow/samtools/samtools_stats/main.nf @@ -3295,9 +3295,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_stats", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_stats/nextflow_schema.json b/target/nextflow/samtools/samtools_stats/nextflow_schema.json index 147c8c22..4e161ad1 100644 --- a/target/nextflow/samtools/samtools_stats/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_stats/nextflow_schema.json @@ -60,7 +60,7 @@ "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" + "default":false } @@ -71,7 +71,7 @@ "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" + "default":false } @@ -202,7 +202,7 @@ "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" + "default":false } @@ -213,7 +213,7 @@ "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" + "default":false } @@ -264,7 +264,7 @@ "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" + "default":"$id.$key.output.txt" } diff --git a/target/nextflow/samtools/samtools_view/.config.vsh.yaml b/target/nextflow/samtools/samtools_view/.config.vsh.yaml index d5495975..50f9b5d3 100644 --- a/target/nextflow/samtools/samtools_view/.config.vsh.yaml +++ b/target/nextflow/samtools/samtools_view/.config.vsh.yaml @@ -665,9 +665,9 @@ build_info: output: "target/nextflow/samtools/samtools_view" executable: "target/nextflow/samtools/samtools_view/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/samtools/samtools_view/main.nf b/target/nextflow/samtools/samtools_view/main.nf index af37fc22..40a8728d 100644 --- a/target/nextflow/samtools/samtools_view/main.nf +++ b/target/nextflow/samtools/samtools_view/main.nf @@ -3476,9 +3476,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/samtools/samtools_view", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/samtools/samtools_view/nextflow_schema.json b/target/nextflow/samtools/samtools_view/nextflow_schema.json index 1de1003b..ef26805a 100644 --- a/target/nextflow/samtools/samtools_view/nextflow_schema.json +++ b/target/nextflow/samtools/samtools_view/nextflow_schema.json @@ -90,7 +90,7 @@ "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" + "default":false } @@ -111,7 +111,7 @@ "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" + "default":"$id.$key.output.bam" } @@ -122,7 +122,7 @@ "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" + "default":false } @@ -133,7 +133,7 @@ "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" + "default":false } @@ -144,7 +144,7 @@ "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" + "default":false } @@ -155,7 +155,7 @@ "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" + "default":false } @@ -166,7 +166,7 @@ "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" + "default":false } @@ -177,7 +177,7 @@ "description": "Type: `boolean_true`, default: `false`. Output the header only", "help_text": "Type: `boolean_true`, default: `false`. Output the header only.\n" , - "default": "False" + "default":false } @@ -188,7 +188,7 @@ "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" + "default":false } @@ -199,7 +199,7 @@ "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" + "default":false } @@ -220,7 +220,7 @@ "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" + "default":false } @@ -261,7 +261,7 @@ "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" + "default":0 } @@ -282,7 +282,7 @@ "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" + "default":0 } @@ -363,7 +363,7 @@ "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" + "default":false } @@ -404,7 +404,7 @@ "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" + "default":0 } @@ -415,7 +415,7 @@ "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" + "default":false } @@ -426,7 +426,7 @@ "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" + "default":false } @@ -447,7 +447,7 @@ "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" + "default":false } @@ -488,7 +488,7 @@ "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" + "default":false } diff --git a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml index e8e7af74..45d3777c 100644 --- a/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_sample/.config.vsh.yaml @@ -173,9 +173,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_sample" executable: "target/nextflow/seqtk/seqtk_sample/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/seqtk/seqtk_sample/main.nf b/target/nextflow/seqtk/seqtk_sample/main.nf index 2d32cc51..2c87f2dc 100644 --- a/target/nextflow/seqtk/seqtk_sample/main.nf +++ b/target/nextflow/seqtk/seqtk_sample/main.nf @@ -3030,9 +3030,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_sample", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json index b91612c2..34bd4219 100644 --- a/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_sample/nextflow_schema.json @@ -40,7 +40,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. The output FASTA/Q file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -81,7 +81,7 @@ "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" + "default":false } diff --git a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml index a29f1fb6..8807886a 100644 --- a/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml +++ b/target/nextflow/seqtk/seqtk_subseq/.config.vsh.yaml @@ -196,9 +196,9 @@ build_info: output: "target/nextflow/seqtk/seqtk_subseq" executable: "target/nextflow/seqtk/seqtk_subseq/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/seqtk/seqtk_subseq/main.nf b/target/nextflow/seqtk/seqtk_subseq/main.nf index 5d1b247f..d5da1598 100644 --- a/target/nextflow/seqtk/seqtk_subseq/main.nf +++ b/target/nextflow/seqtk/seqtk_subseq/main.nf @@ -3060,9 +3060,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/seqtk/seqtk_subseq", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json index f4459a8d..d5f9f16a 100644 --- a/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json +++ b/target/nextflow/seqtk/seqtk_subseq/nextflow_schema.json @@ -50,7 +50,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.fa`. The output FASTA/Q file", "help_text": "Type: `file`, required, default: `$id.$key.output.fa`. The output FASTA/Q file." , - "default": "$id.$key.output.fa" + "default":"$id.$key.output.fa" } @@ -71,7 +71,7 @@ "description": "Type: `boolean_true`, default: `false`. TAB delimited output", "help_text": "Type: `boolean_true`, default: `false`. TAB delimited output." , - "default": "False" + "default":false } @@ -82,7 +82,7 @@ "description": "Type: `boolean_true`, default: `false`. Strand aware", "help_text": "Type: `boolean_true`, default: `false`. Strand aware." , - "default": "False" + "default":false } diff --git a/target/nextflow/sgdemux/.config.vsh.yaml b/target/nextflow/sgdemux/.config.vsh.yaml index 56b02ee0..4161714b 100644 --- a/target/nextflow/sgdemux/.config.vsh.yaml +++ b/target/nextflow/sgdemux/.config.vsh.yaml @@ -429,9 +429,9 @@ build_info: output: "target/nextflow/sgdemux" executable: "target/nextflow/sgdemux/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/sgdemux/main.nf b/target/nextflow/sgdemux/main.nf index 49769671..2defb908 100644 --- a/target/nextflow/sgdemux/main.nf +++ b/target/nextflow/sgdemux/main.nf @@ -3303,9 +3303,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sgdemux", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/sgdemux/nextflow_schema.json b/target/nextflow/sgdemux/nextflow_schema.json index 96d808c2..b295e944 100644 --- a/target/nextflow/sgdemux/nextflow_schema.json +++ b/target/nextflow/sgdemux/nextflow_schema.json @@ -80,7 +80,7 @@ "description": "Type: `boolean_true`, default: `false`. Filter out control reads", "help_text": "Type: `boolean_true`, default: `false`. Filter out control reads" , - "default": "False" + "default":false } @@ -91,7 +91,7 @@ "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" + "default":false } @@ -100,9 +100,7 @@ "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", - "enum": ["T", "B", "S", "M"] - + "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" } @@ -146,7 +144,7 @@ "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" + "default":false } @@ -157,7 +155,7 @@ "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" + "default":false } @@ -228,7 +226,7 @@ "description": "Type: `file`, required, default: `$id.$key.sample_fastq.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files", "help_text": "Type: `file`, required, default: `$id.$key.sample_fastq.sample_fastq`, example: `output`. The directory containing demultiplexed sample FASTQ files." , - "default": "$id.$key.sample_fastq.sample_fastq" + "default":"$id.$key.sample_fastq.sample_fastq" } @@ -239,7 +237,7 @@ "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" + "default":"$id.$key.metrics.tsv" } @@ -250,7 +248,7 @@ "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" + "default":"$id.$key.most_frequent_unmatched.tsv" } @@ -261,7 +259,7 @@ "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" + "default":"$id.$key.sample_barcode_hop_metrics.tsv" } @@ -272,7 +270,7 @@ "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" + "default":"$id.$key.per_project_metrics.tsv" } @@ -283,7 +281,7 @@ "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" + "default":"$id.$key.per_sample_metrics.tsv" } diff --git a/target/nextflow/snpeff/.config.vsh.yaml b/target/nextflow/snpeff/.config.vsh.yaml index cb2c7a3e..b597724e 100644 --- a/target/nextflow/snpeff/.config.vsh.yaml +++ b/target/nextflow/snpeff/.config.vsh.yaml @@ -628,9 +628,9 @@ build_info: output: "target/nextflow/snpeff" executable: "target/nextflow/snpeff/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/snpeff/main.nf b/target/nextflow/snpeff/main.nf index 3f5f264a..3bfe5c5b 100644 --- a/target/nextflow/snpeff/main.nf +++ b/target/nextflow/snpeff/main.nf @@ -3555,9 +3555,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/snpeff", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/snpeff/nextflow_schema.json b/target/nextflow/snpeff/nextflow_schema.json index d86a4de3..2b4f5c52 100644 --- a/target/nextflow/snpeff/nextflow_schema.json +++ b/target/nextflow/snpeff/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.output.vcf" } @@ -61,7 +61,7 @@ "description": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory", "help_text": "Type: `file`, default: `$id.$key.summary.summary`, example: `summary_dir`. Summary file directory." , - "default": "$id.$key.summary.summary" + "default":"$id.$key.summary.summary" } @@ -72,7 +72,7 @@ "description": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory", "help_text": "Type: `file`, default: `$id.$key.genes.genes`, example: `genes_dir`. Txt file directory." , - "default": "$id.$key.genes.genes" + "default":"$id.$key.genes.genes" } @@ -103,7 +103,7 @@ "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" + "default":false } @@ -124,7 +124,7 @@ "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" + "default":false } @@ -145,7 +145,7 @@ "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" + "default":false } @@ -166,7 +166,7 @@ "description": "Type: `boolean_true`, default: `false`. Create HTML summary file", "help_text": "Type: `boolean_true`, default: `false`. Create HTML summary file." , - "default": "False" + "default":false } @@ -177,7 +177,7 @@ "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" + "default":false } @@ -208,7 +208,7 @@ "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" + "default":false } @@ -219,7 +219,7 @@ "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" + "default":false } @@ -230,7 +230,7 @@ "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" + "default":false } @@ -241,7 +241,7 @@ "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" + "default":false } @@ -252,7 +252,7 @@ "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" + "default":false } @@ -283,7 +283,7 @@ "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" + "default":false } @@ -314,7 +314,7 @@ "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" + "default":false } @@ -325,7 +325,7 @@ "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" + "default":false } @@ -336,7 +336,7 @@ "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" + "default":false } @@ -347,7 +347,7 @@ "description": "Type: `boolean_true`, default: `false`. Use old HGVS notation", "help_text": "Type: `boolean_true`, default: `false`. Use old HGVS notation." , - "default": "False" + "default":false } @@ -358,7 +358,7 @@ "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" + "default":false } @@ -369,7 +369,7 @@ "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" + "default":false } @@ -380,7 +380,7 @@ "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" + "default":false } @@ -391,7 +391,7 @@ "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" + "default":false } @@ -402,7 +402,7 @@ "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" + "default":false } @@ -413,7 +413,7 @@ "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" + "default":false } @@ -424,7 +424,7 @@ "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" + "default":false } @@ -435,7 +435,7 @@ "description": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms", "help_text": "Type: `boolean_true`, default: `false`. Use Sequence Ontology terms." , - "default": "False" + "default":false } @@ -476,7 +476,7 @@ "description": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)", "help_text": "Type: `boolean_true`, default: `false`. Debug mode (very verbose)." , - "default": "False" + "default":false } @@ -497,7 +497,7 @@ "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" + "default":false } @@ -508,7 +508,7 @@ "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" + "default":false } @@ -519,7 +519,7 @@ "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" + "default":false } @@ -530,7 +530,7 @@ "description": "Type: `boolean_true`, default: `false`. Verbose mode", "help_text": "Type: `boolean_true`, default: `false`. Verbose mode." , - "default": "False" + "default":false } @@ -551,7 +551,7 @@ "description": "Type: `boolean_true`, default: `false`. Only use canonical transcripts", "help_text": "Type: `boolean_true`, default: `false`. Only use canonical transcripts." , - "default": "False" + "default":false } @@ -582,7 +582,7 @@ "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" + "default":false } @@ -593,7 +593,7 @@ "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" + "default":false } @@ -624,7 +624,7 @@ "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" + "default":false } @@ -635,7 +635,7 @@ "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" + "default":false } @@ -646,7 +646,7 @@ "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" + "default":false } @@ -657,7 +657,7 @@ "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" + "default":false } @@ -668,7 +668,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable inteaction annotations", "help_text": "Type: `boolean_true`, default: `false`. Disable inteaction annotations." , - "default": "False" + "default":false } @@ -679,7 +679,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable motif annotations", "help_text": "Type: `boolean_true`, default: `false`. Disable motif annotations." , - "default": "False" + "default":false } @@ -690,7 +690,7 @@ "description": "Type: `boolean_true`, default: `false`. Disable NextProt annotations", "help_text": "Type: `boolean_true`, default: `false`. Disable NextProt annotations." , - "default": "False" + "default":false } @@ -701,7 +701,7 @@ "description": "Type: `boolean_true`, default: `false`. Only use regulation tracks", "help_text": "Type: `boolean_true`, default: `false`. Only use regulation tracks." , - "default": "False" + "default":false } @@ -712,7 +712,7 @@ "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" + "default":false } @@ -783,7 +783,7 @@ "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" + "default":false } diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 4b8fc1f6..fff395c0 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -594,9 +594,9 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 9bafb9d8..ba848a9f 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3460,9 +3460,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/sortmerna/nextflow_schema.json b/target/nextflow/sortmerna/nextflow_schema.json index d9bfdadb..c0e0df62 100644 --- a/target/nextflow/sortmerna/nextflow_schema.json +++ b/target/nextflow/sortmerna/nextflow_schema.json @@ -20,7 +20,7 @@ "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" + "default":false } @@ -71,7 +71,7 @@ "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" + "default":"$id.$key.log.log" } @@ -82,7 +82,7 @@ "description": "Type: `file`, default: `$id.$key.output.output`. Directory and file prefix for aligned output", "help_text": "Type: `file`, default: `$id.$key.output.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.output" + "default":"$id.$key.output.output" } @@ -93,7 +93,7 @@ "description": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix", "help_text": "Type: `file`, default: `$id.$key.other.other`. Create Non-aligned reads output file with this path/prefix. Must be used with fastx." , - "default": "$id.$key.other.other" + "default":"$id.$key.other.other" } @@ -144,7 +144,7 @@ "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" + "default":false } @@ -155,7 +155,7 @@ "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" + "default":false } @@ -166,7 +166,7 @@ "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" + "default":false } @@ -209,7 +209,7 @@ "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" + "default":false } @@ -220,7 +220,7 @@ "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" + "default":false } @@ -231,7 +231,7 @@ "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" + "default":false } @@ -242,7 +242,7 @@ "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" + "default":false } @@ -253,7 +253,7 @@ "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" + "default":false } @@ -346,7 +346,7 @@ "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" + "default":false } @@ -357,7 +357,7 @@ "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" + "default":false } @@ -388,7 +388,7 @@ "description": "Type: `boolean_true`, default: `false`. Verbose output", "help_text": "Type: `boolean_true`, default: `false`. Verbose output." , - "default": "False" + "default":false } @@ -429,7 +429,7 @@ "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" + "default":false } @@ -440,7 +440,7 @@ "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" + "default":false } @@ -491,7 +491,7 @@ "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" + "default":false } diff --git a/target/nextflow/star/star_align_reads/.config.vsh.yaml b/target/nextflow/star/star_align_reads/.config.vsh.yaml index 2723c123..86213b48 100644 --- a/target/nextflow/star/star_align_reads/.config.vsh.yaml +++ b/target/nextflow/star/star_align_reads/.config.vsh.yaml @@ -2663,9 +2663,9 @@ build_info: output: "target/nextflow/star/star_align_reads" executable: "target/nextflow/star/star_align_reads/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/star/star_align_reads/main.nf b/target/nextflow/star/star_align_reads/main.nf index 8057868b..97daee43 100644 --- a/target/nextflow/star/star_align_reads/main.nf +++ b/target/nextflow/star/star_align_reads/main.nf @@ -5943,9 +5943,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_align_reads", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/star/star_align_reads/nextflow_schema.json b/target/nextflow/star/star_align_reads/nextflow_schema.json index 7afc49c8..b839aa83 100644 --- a/target/nextflow/star/star_align_reads/nextflow_schema.json +++ b/target/nextflow/star/star_align_reads/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":"$id.$key.aligned_reads.bam" } @@ -61,7 +61,7 @@ "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" + "default":"$id.$key.reads_per_gene.tsv" } @@ -72,7 +72,7 @@ "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" + "default":"$id.$key.unmapped.fastq" } @@ -83,7 +83,7 @@ "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" + "default":"$id.$key.unmapped_r2.fastq" } @@ -94,7 +94,7 @@ "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" + "default":"$id.$key.chimeric_junctions.tsv" } @@ -105,7 +105,7 @@ "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" + "default":"$id.$key.log.txt" } @@ -116,7 +116,7 @@ "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" + "default":"$id.$key.splice_junctions.tsv" } @@ -127,7 +127,7 @@ "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" + "default":"$id.$key.reads_aligned_to_transcriptome.bam" } diff --git a/target/nextflow/star/star_genome_generate/.config.vsh.yaml b/target/nextflow/star/star_genome_generate/.config.vsh.yaml index 288d0cff..2a127406 100644 --- a/target/nextflow/star/star_genome_generate/.config.vsh.yaml +++ b/target/nextflow/star/star_genome_generate/.config.vsh.yaml @@ -333,9 +333,9 @@ build_info: output: "target/nextflow/star/star_genome_generate" executable: "target/nextflow/star/star_genome_generate/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/star/star_genome_generate/main.nf b/target/nextflow/star/star_genome_generate/main.nf index 72211a49..17e745a0 100644 --- a/target/nextflow/star/star_genome_generate/main.nf +++ b/target/nextflow/star/star_genome_generate/main.nf @@ -3195,9 +3195,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/star/star_genome_generate", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/star/star_genome_generate/nextflow_schema.json b/target/nextflow/star/star_genome_generate/nextflow_schema.json index 60ab837b..e8aadf16 100644 --- a/target/nextflow/star/star_genome_generate/nextflow_schema.json +++ b/target/nextflow/star/star_genome_generate/nextflow_schema.json @@ -190,7 +190,7 @@ "description": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory", "help_text": "Type: `file`, required, default: `$id.$key.index.index`. STAR index directory." , - "default": "$id.$key.index.index" + "default":"$id.$key.index.index" } diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index f2b1494a..a46f4921 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -770,9 +770,9 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index f9b9b847..c46ce511 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3560,9 +3560,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", diff --git a/target/nextflow/trimgalore/nextflow_schema.json b/target/nextflow/trimgalore/nextflow_schema.json index 99334938..9ee3b485 100644 --- a/target/nextflow/trimgalore/nextflow_schema.json +++ b/target/nextflow/trimgalore/nextflow_schema.json @@ -50,7 +50,7 @@ "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" + "default":false } @@ -61,7 +61,7 @@ "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" + "default":false } @@ -72,7 +72,7 @@ "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" + "default":false } @@ -143,7 +143,7 @@ "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" + "default":false } @@ -154,7 +154,7 @@ "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" + "default":false } @@ -165,7 +165,7 @@ "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" + "default":false } @@ -176,7 +176,7 @@ "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" + "default":false } @@ -227,7 +227,7 @@ "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" + "default":false } @@ -238,7 +238,7 @@ "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" + "default":false } @@ -269,7 +269,7 @@ "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" + "default":false } @@ -280,7 +280,7 @@ "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" + "default":false } @@ -291,7 +291,7 @@ "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" + "default":false } @@ -392,7 +392,7 @@ "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" + "default":false } @@ -403,7 +403,7 @@ "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" + "default":false } @@ -414,7 +414,7 @@ "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" + "default":false } @@ -435,7 +435,7 @@ "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" + "default":false } @@ -446,7 +446,7 @@ "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" + "default":false } @@ -457,7 +457,7 @@ "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" + "default":false } @@ -478,7 +478,7 @@ "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" + "default":false } @@ -489,7 +489,7 @@ "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" + "default":false } @@ -530,7 +530,7 @@ "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory", "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. If specified all output will be written to this directory instead of the current directory." , - "default": "$id.$key.output_dir.output_dir" + "default":"$id.$key.output_dir.output_dir" } @@ -541,7 +541,7 @@ "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" + "default":"$id.$key.trimmed_r1.fastq" } @@ -552,7 +552,7 @@ "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" + "default":"$id.$key.trimmed_r2.fastq" } @@ -563,7 +563,7 @@ "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" + "default":"$id.$key.trimming_report_r1.txt" } @@ -574,7 +574,7 @@ "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" + "default":"$id.$key.trimming_report_r2.txt" } @@ -585,7 +585,7 @@ "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" + "default":"$id.$key.trimmed_fastqc_html_1.html" } @@ -596,7 +596,7 @@ "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" + "default":"$id.$key.trimmed_fastqc_html_2.html" } @@ -607,7 +607,7 @@ "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" + "default":"$id.$key.trimmed_fastqc_zip_1.zip" } @@ -618,7 +618,7 @@ "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" + "default":"$id.$key.trimmed_fastqc_zip_2.zip" } @@ -629,7 +629,7 @@ "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" + "default":"$id.$key.unpaired_r1.fastq" } @@ -640,7 +640,7 @@ "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" + "default":"$id.$key.unpaired_r2.fastq" } 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 0cd39bb2..6296dff4 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml @@ -611,9 +611,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_dedup" executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/umi_tools/umi_tools_dedup/main.nf b/target/nextflow/umi_tools/umi_tools_dedup/main.nf index 4540ecfe..910e67d1 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/main.nf +++ b/target/nextflow/umi_tools/umi_tools_dedup/main.nf @@ -3487,9 +3487,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_dedup", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 834b53ae..58ecde0e 100644 --- a/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json @@ -30,7 +30,7 @@ "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" + "default":false } @@ -71,7 +71,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -82,7 +82,7 @@ "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" + "default":false } @@ -93,7 +93,7 @@ "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" + "default":false } @@ -228,7 +228,7 @@ "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" + "default":false } @@ -259,7 +259,7 @@ "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" + "default":false } @@ -280,7 +280,7 @@ "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" + "default":false } @@ -321,7 +321,7 @@ "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" + "default":false } @@ -342,7 +342,7 @@ "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" + "default":false } @@ -407,7 +407,7 @@ "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" + "default":false } @@ -448,7 +448,7 @@ "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" + "default":false } @@ -459,7 +459,7 @@ "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" + "default":false } @@ -490,7 +490,7 @@ "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" + "default":false } 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 2a04ee4e..dea32d25 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml @@ -434,9 +434,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_extract" executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/umi_tools/umi_tools_extract/main.nf b/target/nextflow/umi_tools/umi_tools_extract/main.nf index c392b782..af503a79 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/main.nf +++ b/target/nextflow/umi_tools/umi_tools_extract/main.nf @@ -3299,9 +3299,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_extract", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 aacd7d1b..927e039b 100644 --- a/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json @@ -70,7 +70,7 @@ "description": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1", "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1." , - "default": "$id.$key.output.output" + "default":"$id.$key.output.output" } @@ -81,7 +81,7 @@ "description": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2." , - "default": "$id.$key.read2_out.read2_out" + "default":"$id.$key.read2_out.read2_out" } @@ -134,7 +134,7 @@ "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" + "default":false } @@ -207,7 +207,7 @@ "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" + "default":false } @@ -218,7 +218,7 @@ "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})$`.\n" , - "default": "False" + "default":false } @@ -229,7 +229,7 @@ "description": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes", "help_text": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is required if the suffixes are not whitespace\nseparated from the rest of the read name.\narguments:\n" , - "default": "False" + "default":false } @@ -272,7 +272,7 @@ "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information", "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information." , - "default": "$id.$key.log.log" + "default":"$id.$key.log.log" } @@ -283,7 +283,7 @@ "description": "Type: `boolean_true`, default: `false`. Send logging information to stderr", "help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr." , - "default": "False" + "default":false } @@ -304,7 +304,7 @@ "description": "Type: `file`, default: `$id.$key.error.error`. File with error information", "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information." , - "default": "$id.$key.error.error" + "default":"$id.$key.error.error" } @@ -335,7 +335,7 @@ "description": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file", "help_text": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file." , - "default": "$id.$key.timeit.timeit" + "default":"$id.$key.timeit.timeit" } @@ -346,7 +346,7 @@ "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" + "default":"all" } @@ -357,7 +357,7 @@ "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" + "default":false } 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 aacf4b2c..30bbe4a2 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/.config.vsh.yaml @@ -256,9 +256,9 @@ build_info: output: "target/nextflow/umi_tools/umi_tools_prepareforrsem" executable: "target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf" viash_version: "0.9.0" - git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" - git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" - git_tag: "v0.2.0-26-ga13b57d" + git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b" + git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox" + git_tag: "v0.2.0-27-g952ff08" package_config: name: "biobox" version: "main" diff --git a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf index 2412e045..df5b652b 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf @@ -3121,9 +3121,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/umi_tools/umi_tools_prepareforrsem", "viash_version" : "0.9.0", - "git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", - "git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", - "git_tag" : "v0.2.0-26-ga13b57d" + "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b", + "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox", + "git_tag" : "v0.2.0-27-g952ff08" }, "package_config" : { "name" : "biobox", 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 75b3c8d5..d7e1cd71 100644 --- a/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json +++ b/target/nextflow/umi_tools/umi_tools_prepareforrsem/nextflow_schema.json @@ -40,7 +40,7 @@ "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.$key.output.bam" + "default":"$id.$key.output.bam" } @@ -51,7 +51,7 @@ "description": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]", "help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information [default = stdout]." , - "default": "$id.$key.log.log" + "default":"$id.$key.log.log" } @@ -62,7 +62,7 @@ "description": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]", "help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information [default = stderr]." , - "default": "$id.$key.error.error" + "default":"$id.$key.error.error" } @@ -73,7 +73,7 @@ "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" + "default":false } @@ -124,7 +124,7 @@ "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" + "default":false } @@ -155,7 +155,7 @@ "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" + "default":false }