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Build branch main with version main (5f6516e)

Browse Source 
Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements
This commit is contained in:
CI
2025-03-06 09:35:27 +00:00
parent 6f8d68b9cc
commit a518d2ead8
343 changed files with 40275 additions and 18530 deletions
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13
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
View File

@@ -123,6 +123,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -231,16 +234,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.0"
git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-27-g952ff08"
viash_version: "0.9.2"
git_commit: "5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-30-g5f6516e"
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"
viash_version: "0.9.2"
source: "src"
target: "target"
config_mods:

172
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
View File

@@ -2,7 +2,7 @@
# bedtools_getfasta main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
@@ -172,76 +172,6 @@ VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_getfasta main"
echo ""
echo "Extract sequences from a FASTA file for each of the intervals defined in a"
echo "BED/GFF/VCF file."
echo ""
echo "Input arguments:"
echo " --input_fasta"
echo " type: file, file must exist"
echo " FASTA file containing sequences for each interval specified in the input"
echo " BED file."
echo " The headers in the input FASTA file must exactly match the chromosome"
echo " column in the BED file."
echo ""
echo " --input_bed"
echo " type: file, file must exist"
echo " BED file containing intervals to extract from the FASTA file."
echo " BED files containing a single region require a newline character"
echo " at the end of the line, otherwise a blank output file is produced."
echo ""
echo " --rna"
echo " type: boolean_true"
echo " The FASTA is RNA not DNA. Reverse complementation handled accordingly."
echo ""
echo "Run arguments:"
echo " -s, --strandedness"
echo " type: boolean_true"
echo " Force strandedness. If the feature occupies the antisense strand, the"
echo " output sequence will"
echo " be reverse complemented. By default strandedness is not taken into"
echo " account."
echo ""
echo "Output arguments:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output file where the output from the 'bedtools getfasta' commend will"
echo " be written to."
echo ""
echo " --tab"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited format instead of in FASTA"
echo " format."
echo ""
echo " --bed_out"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited BED format instead of in"
echo " FASTA format."
echo ""
echo " --name"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\" and"
echo " coordinate columns from the BED feature."
echo ""
echo " --name_only"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\""
echo " columns from the BED feature."
echo ""
echo " --split"
echo " type: boolean_true"
echo " When --input is in BED12 format, create a separate fasta entry for each"
echo " block in a BED12 record,"
echo " blocks being described in the 11th and 12th column of the BED."
echo ""
echo " --full_header"
echo " type: boolean_true"
echo " Use full fasta header. By default, only the word before the first space"
echo " or tab is used."
}
# initialise variables
VIASH_MODE='run'
@@ -526,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:43Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -643,6 +573,102 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_getfasta main"
echo ""
echo "Extract sequences from a FASTA file for each of the intervals defined in a"
echo "BED/GFF/VCF file."
echo ""
echo "Input arguments:"
echo " --input_fasta"
echo " type: file, file must exist"
echo " FASTA file containing sequences for each interval specified in the input"
echo " BED file."
echo " The headers in the input FASTA file must exactly match the chromosome"
echo " column in the BED file."
echo ""
echo " --input_bed"
echo " type: file, file must exist"
echo " BED file containing intervals to extract from the FASTA file."
echo " BED files containing a single region require a newline character"
echo " at the end of the line, otherwise a blank output file is produced."
echo ""
echo " --rna"
echo " type: boolean_true"
echo " The FASTA is RNA not DNA. Reverse complementation handled accordingly."
echo ""
echo "Run arguments:"
echo " -s, --strandedness"
echo " type: boolean_true"
echo " Force strandedness. If the feature occupies the antisense strand, the"
echo " output sequence will"
echo " be reverse complemented. By default strandedness is not taken into"
echo " account."
echo ""
echo "Output arguments:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output file where the output from the 'bedtools getfasta' commend will"
echo " be written to."
echo ""
echo " --tab"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited format instead of in FASTA"
echo " format."
echo ""
echo " --bed_out"
echo " type: boolean_true"
echo " Report extract sequences in a tab-delimited BED format instead of in"
echo " FASTA format."
echo ""
echo " --name"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\" and"
echo " coordinate columns from the BED feature."
echo ""
echo " --name_only"
echo " type: boolean_true"
echo " Set the FASTA header for each extracted sequence to be the \"name\""
echo " columns from the BED feature."
echo ""
echo " --split"
echo " type: boolean_true"
echo " When --input is in BED12 format, create a separate fasta entry for each"
echo " block in a BED12 record,"
echo " blocks being described in the 11th and 12th column of the BED."
echo ""
echo " --full_header"
echo " type: boolean_true"
echo " Use full fasta header. By default, only the word before the first space"
echo " or tab is used."
echo ""
echo "Viash built in Computational Requirements:"
echo " ---cpus=INT"
echo " Number of CPUs to use"
echo " ---memory=STRING"
echo " Amount of memory to use. Examples: 4GB, 3MiB."
echo ""
echo "Viash built in Docker:"
echo " ---setup=STRATEGY"
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
echo " Default: ifneedbepullelsecachedbuild"
echo " ---dockerfile"
echo " Print the dockerfile to stdout."
echo " ---docker_run_args=ARG"
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
echo " ---docker_image_id"
echo " Print the docker image id to stdout."
echo " ---debug"
echo " Enter the docker container for debugging purposes."
echo ""
echo "Viash built in Engines:"
echo " ---engine=ENGINE_ID"
echo " Specify the engine to use. Options are: docker, native."
echo " Default: docker"
}
# initialise array
VIASH_POSITIONAL_ARGS=''