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Build branch main with version main (52f44f5)

Browse Source 
Build pipeline: viash-hub.biobox.main-xrs9m

Source commit: 52f44f5049

Source message: Add agat sp add introns (#104)

* add help

* add config

* add run script

* add test data and expected output + script to fetch them

* add tests

* update changelog

* Update src/agat/agat_sp_add_introns/config.vsh.yaml

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>

* Update src/agat/agat_sp_add_introns/config.vsh.yaml

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>

* Update src/agat/agat_sp_add_introns/config.vsh.yaml

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>

* # create temporary directory and clean up on exit

* add set -e to test

* fix create temporary directory

* fix create temporary directory

* add set -eo pipefail to test

* add set -eo pipefail to script

* remove file added by mistake

* update --config description

* cleanup changelog

* cleanup changelog

* minor changes to config

* reduce test data size

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Co-authored-by: Emma Rousseau <emmarou1@icloud.com>
This commit is contained in:
CI
2024-10-26 13:31:11 +00:00
parent 5ae0d0b0ba
commit 35f315e911
299 changed files with 12788 additions and 749 deletions
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6
target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
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@@ -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: "6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
git_remote: "https://x-access-token:ghs_yMJ96XEhcHROF2pqaopOfHbmZnWq3J2wWhaj@github.com/viash-hub/biobox"
git_tag: "v0.2.0-12-g6e6b139"
git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
git_tag: "v0.2.0-14-g52f44f5"
package_config:
name: "biobox"
version: "main"

4
target/executable/bcftools/bcftools_annotate/bcftools_annotate
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@@ -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="2024-10-26T09:56:42Z"
LABEL org.opencontainers.image.created="2024-10-26T13:11:12Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/bcftools/bcftools_concat/.config.vsh.yaml
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@@ -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: "6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
git_remote: "https://x-access-token:ghs_yMJ96XEhcHROF2pqaopOfHbmZnWq3J2wWhaj@github.com/viash-hub/biobox"
git_tag: "v0.2.0-12-g6e6b139"
git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
git_tag: "v0.2.0-14-g52f44f5"
package_config:
name: "biobox"
version: "main"

4
target/executable/bcftools/bcftools_concat/bcftools_concat
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@@ -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="2024-10-26T09:56:43Z"
LABEL org.opencontainers.image.created="2024-10-26T13:11:13Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/bcftools/bcftools_norm/.config.vsh.yaml
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@@ -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: "6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
git_remote: "https://x-access-token:ghs_yMJ96XEhcHROF2pqaopOfHbmZnWq3J2wWhaj@github.com/viash-hub/biobox"
git_tag: "v0.2.0-12-g6e6b139"
git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
git_tag: "v0.2.0-14-g52f44f5"
package_config:
name: "biobox"
version: "main"

4
target/executable/bcftools/bcftools_norm/bcftools_norm
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@@ -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="2024-10-26T09:56:44Z"
LABEL org.opencontainers.image.created="2024-10-26T13:11:14Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/bcftools/bcftools_sort/.config.vsh.yaml
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@@ -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: "6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
git_remote: "https://x-access-token:ghs_yMJ96XEhcHROF2pqaopOfHbmZnWq3J2wWhaj@github.com/viash-hub/biobox"
git_tag: "v0.2.0-12-g6e6b139"
git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
git_tag: "v0.2.0-14-g52f44f5"
package_config:
name: "biobox"
version: "main"

4
target/executable/bcftools/bcftools_sort/bcftools_sort
View File

@@ -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="2024-10-26T09:56:44Z"
LABEL org.opencontainers.image.created="2024-10-26T13:11:14Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

6
target/executable/bcftools/bcftools_stats/.config.vsh.yaml
View File

@@ -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: "6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
git_remote: "https://x-access-token:ghs_yMJ96XEhcHROF2pqaopOfHbmZnWq3J2wWhaj@github.com/viash-hub/biobox"
git_tag: "v0.2.0-12-g6e6b139"
git_commit: "52f44f5049606ac655154cf54ed53fa76b49896f"
git_remote: "https://x-access-token:ghs_Clbt7tbJqVcfiS3VxySrdzjhMh1FWp3VaTFP@github.com/viash-hub/biobox"
git_tag: "v0.2.0-14-g52f44f5"
package_config:
name: "biobox"
version: "main"

4
target/executable/bcftools/bcftools_stats/bcftools_stats
View File

@@ -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="2024-10-26T09:56:43Z"
LABEL org.opencontainers.image.created="2024-10-26T13:11:13Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="6e6b13939c9d719f1cd7ff5a91a6562e0a6e2e29"
LABEL org.opencontainers.image.revision="52f44f5049606ac655154cf54ed53fa76b49896f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER