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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_intersect/.config.vsh.yaml
View File

@@ -301,6 +301,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -409,16 +412,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bedtools/bedtools_intersect"
executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
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:

386
target/executable/bedtools/bedtools_intersect/bedtools_intersect
View File

@@ -2,7 +2,7 @@
# bedtools_intersect 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.
#
@@ -172,183 +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_intersect main"
echo ""
echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
echo "features."
echo "Moreover, it allows one to have fine control as to how the intersections are"
echo "reported."
echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
echo ""
echo "Inputs:"
echo " -a, --input_a"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input file (BED/GFF/VCF/BAM) to be used as the -a file."
echo ""
echo " -b, --input_b"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: input_b.bed"
echo " The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -wa, --write_a"
echo " type: boolean_true"
echo " Write the original A entry for each overlap."
echo ""
echo " -wb, --write_b"
echo " type: boolean_true"
echo " Write the original B entry for each overlap."
echo " Useful for knowing _what_ A overlaps. Restricted by -f and -r."
echo ""
echo " -loj, --left_outer_join"
echo " type: boolean_true"
echo " Perform a \"left outer join\". That is, for each feature in A report each"
echo " overlap with B."
echo " If no overlaps are found, report a NULL feature for B."
echo ""
echo " -wo, --write_overlap"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " Only A features with overlap are reported."
echo ""
echo " -wao, --write_overlap_plus"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " However, A features w/o overlap are also reported with a NULL B"
echo " feature and overlap = 0."
echo ""
echo " -u, --report_A_if_no_overlap"
echo " type: boolean_true"
echo " Write the original A entry _if_ no overlap is found."
echo " - In other words, just report the fact >=1 hit was found."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -c, --number_of_overlaps_A"
echo " type: boolean_true"
echo " For each entry in A, report the number of overlaps with B."
echo " - Reports 0 for A entries that have no overlap with B."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -v, --report_no_overlaps_A"
echo " type: boolean_true"
echo " Only report those entries in A that have _no overlaps_ with B."
echo " - Similar to \"grep -v\" (an homage)."
echo ""
echo " -ubam, --uncompressed_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
echo ""
echo " -s, --same_strand"
echo " type: boolean_true"
echo " Require same strandedness. That is, only report hits in B."
echo " that overlap A on the _same_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -S, --opposite_strand"
echo " type: boolean_true"
echo " Require different strandedness. That is, only report hits in B"
echo " that overlap A on the _opposite_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -f, --min_overlap_A"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of A."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -F, --min_overlap_B"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of B."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -r, --reciprocal_overlap"
echo " type: boolean_true"
echo " Require that the fraction overlap be reciprocal for A AND B."
echo " - In other words, if -f is 0.90 and -r is used, this requires"
echo " that B overlap 90% of A and A _also_ overlaps 90% of B."
echo ""
echo " -e, --either_overlap"
echo " type: boolean_true"
echo " Require that the minimum fraction be satisfied for A OR B."
echo " - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
echo " that either 90% of A is covered OR 10% of B is covered."
echo " Without -e, both fractions would have to be satisfied."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " Provide a genome file to enforce consistent chromosome"
echo " sort order across input files. Only applies when used"
echo " with -sorted option."
echo ""
echo " --nonamecheck"
echo " type: boolean_true"
echo " For sorted data, don't throw an error if the file"
echo " has different naming conventions for the same chromosome"
echo " (e.g., \"chr1\" vs \"chr01\")."
echo ""
echo " --sorted"
echo " type: boolean_true"
echo " Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
echo ""
echo " --names"
echo " type: string"
echo " When using multiple databases, provide an alias"
echo " for each that will appear instead of a fileId when"
echo " also printing the DB record."
echo ""
echo " --filenames"
echo " type: boolean_true"
echo " When using multiple databases, show each complete filename instead of a"
echo " fileId when also printing the DB record."
echo ""
echo " --sortout"
echo " type: boolean_true"
echo " When using multiple databases, sort the output DB hits for each record."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " --nobuf, --no_buffer_output"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
echo ""
echo " --iobuf, --io_buffer_size"
echo " type: integer"
echo " Specify amount of memory to use for input buffer."
echo " Takes an integer argument. Optional suffixes K/M/G supported."
echo " Note: currently has no effect with compressed files."
}
# initialise variables
VIASH_MODE='run'
@@ -633,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
LABEL org.opencontainers.image.created="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:41Z"
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
@@ -750,6 +573,209 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bedtools_intersect main"
echo ""
echo "bedtools intersect allows one to screen for overlaps between two sets of genomic"
echo "features."
echo "Moreover, it allows one to have fine control as to how the intersections are"
echo "reported."
echo "bedtools intersect works with both BED/GFF/VCF and BAM files as input."
echo ""
echo "Inputs:"
echo " -a, --input_a"
echo " type: file, required parameter, file must exist"
echo " example: input_a.bed"
echo " The input file (BED/GFF/VCF/BAM) to be used as the -a file."
echo ""
echo " -b, --input_b"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: input_b.bed"
echo " The input file(s) (BED/GFF/VCF/BAM) to be used as the -b file(s)."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " example: output.bed"
echo " The output BED file."
echo ""
echo "Options:"
echo " -wa, --write_a"
echo " type: boolean_true"
echo " Write the original A entry for each overlap."
echo ""
echo " -wb, --write_b"
echo " type: boolean_true"
echo " Write the original B entry for each overlap."
echo " Useful for knowing _what_ A overlaps. Restricted by -f and -r."
echo ""
echo " -loj, --left_outer_join"
echo " type: boolean_true"
echo " Perform a \"left outer join\". That is, for each feature in A report each"
echo " overlap with B."
echo " If no overlaps are found, report a NULL feature for B."
echo ""
echo " -wo, --write_overlap"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " Only A features with overlap are reported."
echo ""
echo " -wao, --write_overlap_plus"
echo " type: boolean_true"
echo " Write the original A and B entries plus the number of base pairs of"
echo " overlap between the two features."
echo " - Overlaps restricted by -f and -r."
echo " However, A features w/o overlap are also reported with a NULL B"
echo " feature and overlap = 0."
echo ""
echo " -u, --report_A_if_no_overlap"
echo " type: boolean_true"
echo " Write the original A entry _if_ no overlap is found."
echo " - In other words, just report the fact >=1 hit was found."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -c, --number_of_overlaps_A"
echo " type: boolean_true"
echo " For each entry in A, report the number of overlaps with B."
echo " - Reports 0 for A entries that have no overlap with B."
echo " - Overlaps restricted by -f and -r."
echo ""
echo " -v, --report_no_overlaps_A"
echo " type: boolean_true"
echo " Only report those entries in A that have _no overlaps_ with B."
echo " - Similar to \"grep -v\" (an homage)."
echo ""
echo " -ubam, --uncompressed_bam"
echo " type: boolean_true"
echo " Write uncompressed BAM output. Default writes compressed BAM."
echo ""
echo " -s, --same_strand"
echo " type: boolean_true"
echo " Require same strandedness. That is, only report hits in B."
echo " that overlap A on the _same_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -S, --opposite_strand"
echo " type: boolean_true"
echo " Require different strandedness. That is, only report hits in B"
echo " that overlap A on the _opposite_ strand."
echo " - By default, overlaps are reported without respect to strand."
echo ""
echo " -f, --min_overlap_A"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of A."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -F, --min_overlap_B"
echo " type: double"
echo " example: 0.5"
echo " Minimum overlap required as a fraction of B."
echo " - Default is 1E-9 (i.e., 1bp)."
echo " - FLOAT (e.g. 0.50)"
echo ""
echo " -r, --reciprocal_overlap"
echo " type: boolean_true"
echo " Require that the fraction overlap be reciprocal for A AND B."
echo " - In other words, if -f is 0.90 and -r is used, this requires"
echo " that B overlap 90% of A and A _also_ overlaps 90% of B."
echo ""
echo " -e, --either_overlap"
echo " type: boolean_true"
echo " Require that the minimum fraction be satisfied for A OR B."
echo " - In other words, if -e is used with -f 0.90 and -F 0.10 this requires"
echo " that either 90% of A is covered OR 10% of B is covered."
echo " Without -e, both fractions would have to be satisfied."
echo ""
echo " --split"
echo " type: boolean_true"
echo " Treat \"split\" BAM or BED12 entries as distinct BED intervals."
echo ""
echo " -g, --genome"
echo " type: file, file must exist"
echo " example: genome.txt"
echo " Provide a genome file to enforce consistent chromosome"
echo " sort order across input files. Only applies when used"
echo " with -sorted option."
echo ""
echo " --nonamecheck"
echo " type: boolean_true"
echo " For sorted data, don't throw an error if the file"
echo " has different naming conventions for the same chromosome"
echo " (e.g., \"chr1\" vs \"chr01\")."
echo ""
echo " --sorted"
echo " type: boolean_true"
echo " Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input."
echo ""
echo " --names"
echo " type: string"
echo " When using multiple databases, provide an alias"
echo " for each that will appear instead of a fileId when"
echo " also printing the DB record."
echo ""
echo " --filenames"
echo " type: boolean_true"
echo " When using multiple databases, show each complete filename instead of a"
echo " fileId when also printing the DB record."
echo ""
echo " --sortout"
echo " type: boolean_true"
echo " When using multiple databases, sort the output DB hits for each record."
echo ""
echo " --bed"
echo " type: boolean_true"
echo " If using BAM input, write output as BED."
echo ""
echo " --header"
echo " type: boolean_true"
echo " Print the header from the A file prior to results."
echo ""
echo " --nobuf, --no_buffer_output"
echo " type: boolean_true"
echo " Disable buffered output. Using this option will cause each line"
echo " of output to be printed as it is generated, rather than saved"
echo " in a buffer. This will make printing large output files"
echo " noticeably slower, but can be useful in conjunction with"
echo " other software tools and scripts that need to process one"
echo " line of bedtools output at a time."
echo ""
echo " --iobuf, --io_buffer_size"
echo " type: integer"
echo " Specify amount of memory to use for input buffer."
echo " Takes an integer argument. Optional suffixes K/M/G supported."
echo " Note: currently has no effect with compressed files."
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=''