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Build branch main with version main (86333c1)

Browse Source 
Build pipeline: meta-vsh-ci-template-tpwsr

Source commit: 86333c1a46

Source message: SnpEff (#153)

* Help file

* config file

* config file

* runners script

* config file

* test script

* test

* test

* runners script

* snake case

* snake case

* output parameters

* modify argument formatting, container setup

* fix buf with mv command

* avoid boolean_false and fix bug with output files

---------

Co-authored-by: Emma Rousseau <emmarou1@icloud.com>
This commit is contained in:
CI
2024-10-16 09:18:30 +00:00
parent 09f5294af0
commit 55de3a494d
274 changed files with 10661 additions and 715 deletions
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6
target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
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@@ -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="2024-10-07T09:07:56Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:44Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
View File

@@ -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="2024-10-07T09:07:56Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
View File

@@ -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="2024-10-07T09:07:57Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
View File

@@ -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="2024-10-07T09:07:56Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
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@@ -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="2024-10-07T09:07:55Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:46Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
View File

@@ -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: "add125261c6fa0ed7c9906fc85e7368d2072c4a3"
git_remote: "https://x-access-token:ghs_bKg5UFS6ueiPm6KFjDzlVauquRQ8Fx1iMgnZ@github.com/viash-hub/biobox"
git_tag: "v0.2.0-9-gadd1252"
git_commit: "86333c1a465db45facd936695f1f33b186ccf0fc"
git_remote: "https://x-access-token:ghs_ILHMFrZClEMTdFrL0nibETdAJotVbg0IPeJ7@github.com/viash-hub/biobox"
git_tag: "v0.2.0-10-g86333c1"
package_config:
name: "biobox"
version: "main"

4
target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
View File

@@ -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="2024-10-07T09:07:55Z"
LABEL org.opencontainers.image.created="2024-10-16T08:57:45Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="add125261c6fa0ed7c9906fc85e7368d2072c4a3"
LABEL org.opencontainers.image.revision="86333c1a465db45facd936695f1f33b186ccf0fc"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER