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Build branch main with version main (c3ba4a7)

Browse Source 
Build pipeline: viash-hub.biobox.main-n2mwd

Source commit: c3ba4a7849

Source message: Bcftools annotate (#143)

* Initial commit

* Update config.vsh.yaml

* changes in config file

* Update script.sh

* Help File

* Update script.sh

* Update test.sh

* bug fixing and adding tests

* Update test.sh

* Update test.sh

* adding 3rd test

* More tests

* Moreee tests

* Update test.sh

* small changes

* Update CHANGELOG.md

* Update config.vsh.yaml

* bug fixing on config

* Requested changes

---------

Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
This commit is contained in:
CI
2024-09-10 14:11:21 +00:00
parent 0075a8df93
commit db2f4203b8
231 changed files with 8225 additions and 276 deletions
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2
target/executable/samtools/samtools_collate/.config.vsh.yaml
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@@ -264,7 +264,7 @@ build_info:
output: "target/executable/samtools/samtools_collate"
executable: "target/executable/samtools/samtools_collate/samtools_collate"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_collate/samtools_collate
View File

@@ -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="2024-09-10T13:55:41Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_faidx/.config.vsh.yaml
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@@ -243,7 +243,7 @@ build_info:
output: "target/executable/samtools/samtools_faidx"
executable: "target/executable/samtools/samtools_faidx/samtools_faidx"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_faidx/samtools_faidx
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@@ -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="2024-09-10T13:55:41Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_fasta/.config.vsh.yaml
View File

@@ -433,7 +433,7 @@ build_info:
output: "target/executable/samtools/samtools_fasta"
executable: "target/executable/samtools/samtools_fasta/samtools_fasta"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_fasta/samtools_fasta
View File

@@ -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="2024-09-10T13:55:41Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_fastq/.config.vsh.yaml
View File

@@ -433,7 +433,7 @@ build_info:
output: "target/executable/samtools/samtools_fastq"
executable: "target/executable/samtools/samtools_fastq/samtools_fastq"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_fastq/samtools_fastq
View File

@@ -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="2024-09-10T13:55:40Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:00Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_flagstat/.config.vsh.yaml
View File

@@ -173,7 +173,7 @@ build_info:
output: "target/executable/samtools/samtools_flagstat"
executable: "target/executable/samtools/samtools_flagstat/samtools_flagstat"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_flagstat/samtools_flagstat
View File

@@ -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="2024-09-10T13:55:40Z"
LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_idxstats/.config.vsh.yaml
View File

@@ -183,7 +183,7 @@ build_info:
output: "target/executable/samtools/samtools_idxstats"
executable: "target/executable/samtools/samtools_idxstats/samtools_idxstats"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_idxstats/samtools_idxstats
View File

@@ -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="2024-09-10T13:55:39Z"
LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_index/.config.vsh.yaml
View File

@@ -189,7 +189,7 @@ build_info:
output: "target/executable/samtools/samtools_index"
executable: "target/executable/samtools/samtools_index/samtools_index"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_index/samtools_index
View File

@@ -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="2024-09-10T13:55:39Z"
LABEL org.opencontainers.image.created="2024-09-10T13:56:58Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_sort/.config.vsh.yaml
View File

@@ -332,7 +332,7 @@ build_info:
output: "target/executable/samtools/samtools_sort"
executable: "target/executable/samtools/samtools_sort/samtools_sort"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_sort/samtools_sort
View File

@@ -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="2024-09-10T13:55:42Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_stats/.config.vsh.yaml
View File

@@ -401,7 +401,7 @@ build_info:
output: "target/executable/samtools/samtools_stats"
executable: "target/executable/samtools/samtools_stats/samtools_stats"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_stats/samtools_stats
View File

@@ -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="2024-09-10T13:55:42Z"
LABEL org.opencontainers.image.created="2024-09-10T13:57:01Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/samtools/samtools_view/.config.vsh.yaml
View File

@@ -665,7 +665,7 @@ build_info:
output: "target/executable/samtools/samtools_view"
executable: "target/executable/samtools/samtools_view/samtools_view"
viash_version: "0.9.0-RC7"
git_commit: "8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
git_commit: "c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_view/samtools_view
View File

@@ -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="2024-09-10T13:55:40Z"
LABEL org.opencontainers.image.created="2024-09-10T13:56:59Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="8fe9d66b0c689776846dcb0ecb01a30f3ef1b66b"
LABEL org.opencontainers.image.revision="c3ba4a78497f7518725bb7d3e213b2a9bcee511e"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER