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Build branch main with version main (38f635a)

Browse Source 
Build pipeline: viash-hub.biobox.main-dz9k8

Source commit: 38f635ad57

Source message: Add agat convert genscan2gff (#100)

* add config

* add help

* add test data and expected output adn the script to obtain them

* add running script

* add test script

* update changelog

* cleanup

* fix tests

* format description

* remove unused argument --inflate-off

* update --config description

* add requirements

* create temporary directory and clean up on exit

* add GENSCAN in keywords

* add set -e to test

* fix create temporary directory

* add set -eo pipefail to test

* add set -eo pipefail to script

* fix create temporary directory

* update --config description

* cleanup changelog

* cleanup changelog

* Update deprecated variable

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
This commit is contained in:
CI
2024-09-17 07:19:20 +00:00
parent 4b61e09a56
commit f47054953e
255 changed files with 8531 additions and 1561 deletions
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9
target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
View File

@@ -468,15 +468,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_annotate"
executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
viash_version: "0.9.0-RC7"
git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
git_tag: "v0.2.0-2-g38f635a"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_annotate/bcftools_annotate
View File

@@ -2,9 +2,9 @@
# bcftools_annotate main
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -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="2024-09-16T07:55:10Z"
LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

9
target/executable/bcftools/bcftools_concat/.config.vsh.yaml
View File

@@ -334,15 +334,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_concat"
executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
viash_version: "0.9.0-RC7"
git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
git_tag: "v0.2.0-2-g38f635a"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_concat/bcftools_concat
View File

@@ -2,9 +2,9 @@
# bcftools_concat main
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -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="2024-09-16T07:55:10Z"
LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

9
target/executable/bcftools/bcftools_norm/.config.vsh.yaml
View File

@@ -415,15 +415,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_norm"
executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
viash_version: "0.9.0-RC7"
git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
git_tag: "v0.2.0-2-g38f635a"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_norm/bcftools_norm
View File

@@ -2,9 +2,9 @@
# bcftools_norm main
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -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="2024-09-16T07:55:11Z"
LABEL org.opencontainers.image.created="2024-09-17T06:47:29Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

9
target/executable/bcftools/bcftools_sort/.config.vsh.yaml
View File

@@ -184,15 +184,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_sort"
executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
viash_version: "0.9.0-RC7"
git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
git_tag: "v0.2.0-2-g38f635a"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_sort/bcftools_sort
View File

@@ -2,9 +2,9 @@
# bcftools_sort main
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -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="2024-09-16T07:55:09Z"
LABEL org.opencontainers.image.created="2024-09-17T06:47:27Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

9
target/executable/bcftools/bcftools_stats/.config.vsh.yaml
View File

@@ -457,15 +457,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_stats"
executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
viash_version: "0.9.0-RC7"
git_commit: "124d50ce5318b612e4a1e4da1be705523cd6eab7"
git_remote: "https://x-access-token:ghs_royCfknE2TdPwJPOM1bW31Qho8HPrM4SPutG@github.com/viash-hub/biobox"
viash_version: "0.9.0"
git_commit: "38f635ad57ef05550bba3a0864c81627f84f5ad2"
git_remote: "https://x-access-token:ghs_wFnCgH6LWyegjU3sAMvKhUKRQxXHxx2DXwds@github.com/viash-hub/biobox"
git_tag: "v0.2.0-2-g38f635a"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0-RC7"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

10
target/executable/bcftools/bcftools_stats/bcftools_stats
View File

@@ -2,9 +2,9 @@
# bcftools_stats main
#
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -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="2024-09-16T07:55:10Z"
LABEL org.opencontainers.image.created="2024-09-17T06:47:28Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="124d50ce5318b612e4a1e4da1be705523cd6eab7"
LABEL org.opencontainers.image.revision="38f635ad57ef05550bba3a0864c81627f84f5ad2"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER