vsh/biobox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (4aa0a89)

Browse Source 
Build pipeline: viash-hub.biobox.main-rgg5q

Source commit: 4aa0a893d2

Source message: Add agat convert bed2gff (#97)

* add config

* add help

* add script

* add test data and expected output file

* add script to get test data

* add tests

* update changelog

* fix path to test data

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
This commit is contained in:
CI
2024-07-31 19:45:06 +00:00
parent da141b5d98
commit 833a44f68a
166 changed files with 6004 additions and 1832 deletions
Download Patch File Download Diff File Expand all files Collapse all files

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

@@ -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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -518,9 +518,9 @@ 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="2024-07-31T19:24:30Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_faidx/samtools_faidx
View File

@@ -511,9 +511,9 @@ 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="2024-07-31T19:24:31Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:44Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -624,9 +624,9 @@ 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="2024-07-31T19:24:28Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:41Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

4
target/executable/samtools/samtools_fastq/samtools_fastq
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_fastq"
LABEL org.opencontainers.image.created="2024-07-31T19:24:32Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:44Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -473,9 +473,9 @@ 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="2024-07-31T19:24:28Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -477,9 +477,9 @@ 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="2024-07-31T19:24:29Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -484,9 +484,9 @@ 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="2024-07-31T19:24:30Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -555,9 +555,9 @@ 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="2024-07-31T19:24:31Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:43Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -574,9 +574,9 @@ 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="2024-07-31T19:24:29Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:42Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
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-RC6"
git_commit: "de8b4248b64e0d2e04a6f20c35212403c57a1058"
git_commit: "4aa0a893d2f8be5f0d03797afc15a04c53664367"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"

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

@@ -824,9 +824,9 @@ 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="2024-07-31T19:24:27Z"
LABEL org.opencontainers.image.created="2024-07-31T19:27:41Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/samtools"
LABEL org.opencontainers.image.revision="de8b4248b64e0d2e04a6f20c35212403c57a1058"
LABEL org.opencontainers.image.revision="4aa0a893d2f8be5f0d03797afc15a04c53664367"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER