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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/bcftools/bcftools_annotate/.config.vsh.yaml
View File

@@ -355,6 +355,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -468,16 +471,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_annotate"
executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
viash_version: "0.9.0"
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:

420
target/executable/bcftools/bcftools_annotate/bcftools_annotate
View File

@@ -2,7 +2,7 @@
# bcftools_annotate 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.
#
@@ -172,200 +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 "bcftools_annotate main"
echo ""
echo "Add or remove annotations from a VCF/BCF file."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output annotated file."
echo ""
echo "Options:"
echo " For examples on how to use use bcftools annotate see"
echo " http://samtools.github.io/bcftools/howtos/annotate.html."
echo " For more details on the options see"
echo " https://samtools.github.io/bcftools/bcftools.html#annotate."
echo ""
echo " --a, --annotations"
echo " type: file, file must exist"
echo " VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ."
echo ""
echo " --c, --columns"
echo " type: string"
echo " List of columns in the annotation file, e.g."
echo " CHROM,POS,REF,ALT,-,INFO/TAG."
echo " See man page for details."
echo ""
echo " --C, --columns_file"
echo " type: file, file must exist"
echo " Read -c columns from FILE, one name per row, with optional --merge_logic"
echo " TYPE: NAME[ TYPE]."
echo ""
echo " --e, --exclude"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Exclude sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --force"
echo " type: boolean_true"
echo " continue even when parsing errors, such as undefined tags, are"
echo " encountered."
echo " Note this can be an unsafe operation and can result in corrupted BCF"
echo " files."
echo " If this option is used, make sure to sanity check the result thoroughly."
echo ""
echo " --H, --header_line"
echo " type: string"
echo " Header line which should be appended to the VCF header, can be given"
echo " multiple times."
echo ""
echo " --h, --header_lines"
echo " type: file, file must exist"
echo " File with header lines to append to the VCF header."
echo " For example:"
echo " ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example"
echo " header line\">"
echo " ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another"
echo " header line\">"
echo ""
echo " --I, --set_id"
echo " type: string"
echo " Set ID column using a \`bcftools query\`-like expression, see man page for"
echo " details."
echo ""
echo " --include"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Select sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --k, --keep_sites"
echo " type: boolean_true"
echo " Leave --include/--exclude sites unchanged instead of discarding them."
echo ""
echo " --l, --merge_logic"
echo " type: string"
echo " When multiple regions overlap a single record, this option defines how"
echo " to treat multiple annotation values."
echo " See man page for more details."
echo ""
echo " --m, --mark_sites"
echo " type: string"
echo " Annotate sites which are present (\"+\") or absent (\"-\") in the -a file"
echo " with a new INFO/TAG flag."
echo ""
echo " --min_overlap"
echo " type: string"
echo " Minimum overlap required as a fraction of the variant in the annotation"
echo " -a file (ANN),"
echo " in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)."
echo " By default overlaps of arbitrary length are sufficient."
echo " The option can be used only with the tab-delimited annotation -a file"
echo " and with BEG and END columns present."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the output VCF"
echo " header."
echo ""
echo " --O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " --pair_logic"
echo " type: string"
echo " choices: [ snps, indels, both, all, some, exact ]"
echo " Controls how to match records from the annotation file to the target"
echo " VCF."
echo " Effective only when -a is a VCF or BCF file."
echo " The option replaces the former uninuitive --collapse."
echo " See Common Options for more."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " --rename_annotations"
echo " type: file, file must exist"
echo " Rename annotations: TYPE/old\\tnew, where TYPE is one of"
echo " FILTER,INFO,FORMAT."
echo ""
echo " --rename_chromosomes"
echo " type: file, file must exist"
echo " Rename chromosomes according to the map in file, with \"old_name"
echo " new_name\\n\" pairs"
echo " separated by whitespaces, each on a separate line."
echo ""
echo " --samples"
echo " type: string"
echo " Subset of samples to annotate."
echo " See also"
echo " https://samtools.github.io/bcftools/bcftools.html#common_options."
echo ""
echo " --samples_file"
echo " type: file, file must exist"
echo " Subset of samples to annotate in file format."
echo " See also"
echo " https://samtools.github.io/bcftools/bcftools.html#common_options."
echo ""
echo " --single_overlaps"
echo " type: boolean_true"
echo " Use this option to keep memory requirements low with very large"
echo " annotation files."
echo " Note, however, that this comes at a cost, only single overlapping"
echo " intervals are considered in this mode."
echo " This was the default mode until the commit af6f0c9 (Feb 24 2019)."
echo ""
echo " --x, --remove"
echo " type: string"
echo " List of annotations to remove."
echo " Use \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a"
echo " specific filter."
echo " Similarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to"
echo " remove all FORMAT tags except GT."
echo " To remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\""
echo " (and similarly for FORMAT and FILTER)."
echo " \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"."
}
# initialise variables
VIASH_MODE='run'
@@ -650,9 +456,9 @@ 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="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -767,6 +573,226 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcftools_annotate main"
echo ""
echo "Add or remove annotations from a VCF/BCF file."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output annotated file."
echo ""
echo "Options:"
echo " For examples on how to use use bcftools annotate see"
echo " http://samtools.github.io/bcftools/howtos/annotate.html."
echo " For more details on the options see"
echo " https://samtools.github.io/bcftools/bcftools.html#annotate."
echo ""
echo " --a, --annotations"
echo " type: file, file must exist"
echo " VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+ ."
echo ""
echo " --c, --columns"
echo " type: string"
echo " List of columns in the annotation file, e.g."
echo " CHROM,POS,REF,ALT,-,INFO/TAG."
echo " See man page for details."
echo ""
echo " --C, --columns_file"
echo " type: file, file must exist"
echo " Read -c columns from FILE, one name per row, with optional --merge_logic"
echo " TYPE: NAME[ TYPE]."
echo ""
echo " --e, --exclude"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Exclude sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --force"
echo " type: boolean_true"
echo " continue even when parsing errors, such as undefined tags, are"
echo " encountered."
echo " Note this can be an unsafe operation and can result in corrupted BCF"
echo " files."
echo " If this option is used, make sure to sanity check the result thoroughly."
echo ""
echo " --H, --header_line"
echo " type: string"
echo " Header line which should be appended to the VCF header, can be given"
echo " multiple times."
echo ""
echo " --h, --header_lines"
echo " type: file, file must exist"
echo " File with header lines to append to the VCF header."
echo " For example:"
echo " ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example"
echo " header line\">"
echo " ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another"
echo " header line\">"
echo ""
echo " --I, --set_id"
echo " type: string"
echo " Set ID column using a \`bcftools query\`-like expression, see man page for"
echo " details."
echo ""
echo " --include"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Select sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --k, --keep_sites"
echo " type: boolean_true"
echo " Leave --include/--exclude sites unchanged instead of discarding them."
echo ""
echo " --l, --merge_logic"
echo " type: string"
echo " When multiple regions overlap a single record, this option defines how"
echo " to treat multiple annotation values."
echo " See man page for more details."
echo ""
echo " --m, --mark_sites"
echo " type: string"
echo " Annotate sites which are present (\"+\") or absent (\"-\") in the -a file"
echo " with a new INFO/TAG flag."
echo ""
echo " --min_overlap"
echo " type: string"
echo " Minimum overlap required as a fraction of the variant in the annotation"
echo " -a file (ANN),"
echo " in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF)."
echo " By default overlaps of arbitrary length are sufficient."
echo " The option can be used only with the tab-delimited annotation -a file"
echo " and with BEG and END columns present."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the output VCF"
echo " header."
echo ""
echo " --O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " --pair_logic"
echo " type: string"
echo " choices: [ snps, indels, both, all, some, exact ]"
echo " Controls how to match records from the annotation file to the target"
echo " VCF."
echo " Effective only when -a is a VCF or BCF file."
echo " The option replaces the former uninuitive --collapse."
echo " See Common Options for more."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " --rename_annotations"
echo " type: file, file must exist"
echo " Rename annotations: TYPE/old\\tnew, where TYPE is one of"
echo " FILTER,INFO,FORMAT."
echo ""
echo " --rename_chromosomes"
echo " type: file, file must exist"
echo " Rename chromosomes according to the map in file, with \"old_name"
echo " new_name\\n\" pairs"
echo " separated by whitespaces, each on a separate line."
echo ""
echo " --samples"
echo " type: string"
echo " Subset of samples to annotate."
echo " See also"
echo " https://samtools.github.io/bcftools/bcftools.html#common_options."
echo ""
echo " --samples_file"
echo " type: file, file must exist"
echo " Subset of samples to annotate in file format."
echo " See also"
echo " https://samtools.github.io/bcftools/bcftools.html#common_options."
echo ""
echo " --single_overlaps"
echo " type: boolean_true"
echo " Use this option to keep memory requirements low with very large"
echo " annotation files."
echo " Note, however, that this comes at a cost, only single overlapping"
echo " intervals are considered in this mode."
echo " This was the default mode until the commit af6f0c9 (Feb 24 2019)."
echo ""
echo " --x, --remove"
echo " type: string"
echo " List of annotations to remove."
echo " Use \"FILTER\" to remove all filters or \"FILTER/SomeFilter\" to remove a"
echo " specific filter."
echo " Similarly, \"INFO\" can be used to remove all INFO tags and \"FORMAT\" to"
echo " remove all FORMAT tags except GT."
echo " To remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\""
echo " (and similarly for FORMAT and FILTER)."
echo " \"INFO\" can be abbreviated to \"INF\" and \"FORMAT\" to \"FMT\"."
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=''

13
target/executable/bcftools/bcftools_concat/.config.vsh.yaml
View File

@@ -221,6 +221,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -334,16 +337,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_concat"
executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
viash_version: "0.9.0"
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:

252
target/executable/bcftools/bcftools_concat/bcftools_concat
View File

@@ -2,7 +2,7 @@
# bcftools_concat 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.
#
@@ -172,116 +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 "bcftools_concat main"
echo ""
echo "Concatenate or combine VCF/BCF files. All source files must have the same sample"
echo "columns appearing in the same order. The program can be used, for example, to"
echo "concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel"
echo "VCF into one. The input files must be sorted by chr and position. The files"
echo "must be given in the correct order to produce sorted VCF on output unless"
echo "the -a, --allow-overlaps option is specified. With the --naive option, the files"
echo "are concatenated without being recompressed, which is very fast."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, multiple values allowed, file must exist"
echo " Input VCF/BCF files to concatenate."
echo ""
echo " -f, --file_list"
echo " type: file, file must exist"
echo " Read the list of VCF/BCF files from a file, one file name per line."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output concatenated VCF/BCF file."
echo ""
echo "Options:"
echo " -a, --allow_overlaps"
echo " type: boolean_true"
echo " First coordinate of the next file can precede last record of the current"
echo " file."
echo ""
echo " -c, --compact_PS"
echo " type: boolean_true"
echo " Do not output PS tag at each site, only at the start of a new phase set"
echo " block."
echo ""
echo " -d, --remove_duplicates"
echo " type: string"
echo " choices: [ snps, indels, both, all, exact, none ]"
echo " Output duplicate records present in multiple files only once:"
echo " <snps|indels|both|all|exact>."
echo ""
echo " -l, --ligate"
echo " type: boolean_true"
echo " Ligate phased VCFs by matching phase at overlapping haplotypes."
echo ""
echo " --ligate_force"
echo " type: boolean_true"
echo " Ligate even non-overlapping chunks, keep all sites."
echo ""
echo " --ligate_warn"
echo " type: boolean_true"
echo " Drop sites in imperfect overlaps."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the header."
echo ""
echo " -n, --naive"
echo " type: boolean_true"
echo " Concatenate files without recompression, a header check compatibility is"
echo " performed."
echo ""
echo " --naive_force"
echo " type: boolean_true"
echo " Same as --naive, but header compatibility is not checked."
echo " Dangerous, use with caution."
echo ""
echo " -O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " -q, --min_PQ"
echo " type: integer"
echo " example: 30"
echo " Break phase set if phasing quality is lower than <int>."
echo ""
echo " -r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " -R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
}
# initialise variables
VIASH_MODE='run'
@@ -566,9 +456,9 @@ 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="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:36Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -683,6 +573,142 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcftools_concat main"
echo ""
echo "Concatenate or combine VCF/BCF files. All source files must have the same sample"
echo "columns appearing in the same order. The program can be used, for example, to"
echo "concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel"
echo "VCF into one. The input files must be sorted by chr and position. The files"
echo "must be given in the correct order to produce sorted VCF on output unless"
echo "the -a, --allow-overlaps option is specified. With the --naive option, the files"
echo "are concatenated without being recompressed, which is very fast."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, multiple values allowed, file must exist"
echo " Input VCF/BCF files to concatenate."
echo ""
echo " -f, --file_list"
echo " type: file, file must exist"
echo " Read the list of VCF/BCF files from a file, one file name per line."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output concatenated VCF/BCF file."
echo ""
echo "Options:"
echo " -a, --allow_overlaps"
echo " type: boolean_true"
echo " First coordinate of the next file can precede last record of the current"
echo " file."
echo ""
echo " -c, --compact_PS"
echo " type: boolean_true"
echo " Do not output PS tag at each site, only at the start of a new phase set"
echo " block."
echo ""
echo " -d, --remove_duplicates"
echo " type: string"
echo " choices: [ snps, indels, both, all, exact, none ]"
echo " Output duplicate records present in multiple files only once:"
echo " <snps|indels|both|all|exact>."
echo ""
echo " -l, --ligate"
echo " type: boolean_true"
echo " Ligate phased VCFs by matching phase at overlapping haplotypes."
echo ""
echo " --ligate_force"
echo " type: boolean_true"
echo " Ligate even non-overlapping chunks, keep all sites."
echo ""
echo " --ligate_warn"
echo " type: boolean_true"
echo " Drop sites in imperfect overlaps."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the header."
echo ""
echo " -n, --naive"
echo " type: boolean_true"
echo " Concatenate files without recompression, a header check compatibility is"
echo " performed."
echo ""
echo " --naive_force"
echo " type: boolean_true"
echo " Same as --naive, but header compatibility is not checked."
echo " Dangerous, use with caution."
echo ""
echo " -O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " -q, --min_PQ"
echo " type: integer"
echo " example: 30"
echo " Break phase set if phasing quality is lower than <int>."
echo ""
echo " -r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " -R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
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=''

13
target/executable/bcftools/bcftools_norm/.config.vsh.yaml
View File

@@ -302,6 +302,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -415,16 +418,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_norm"
executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
viash_version: "0.9.0"
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:

298
target/executable/bcftools/bcftools_norm/bcftools_norm
View File

@@ -2,7 +2,7 @@
# bcftools_norm 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.
#
@@ -172,139 +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 "bcftools_norm main"
echo ""
echo "Left-align and normalize indels, check if REF alleles match the reference, split"
echo "multiallelic sites into multiple rows;"
echo "recover multiallelics from multiple rows."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output normalized VCF/BCF file."
echo ""
echo "Options:"
echo " -a, --atomize"
echo " type: boolean_true"
echo " Decompose complex variants (e.g., MNVs become consecutive SNVs)."
echo ""
echo " --atom_overlaps"
echo " type: string"
echo " choices: [ ., * ]"
echo " Use the star allele (*) for overlapping alleles or set to missing (.)."
echo ""
echo " -c, --check_ref"
echo " type: string"
echo " choices: [ e, w, x, s ]"
echo " Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad"
echo " sites."
echo ""
echo " -d, --remove_duplicates"
echo " type: string"
echo " choices: [ snps, indels, both, all, exact, none ]"
echo " Remove duplicate snps, indels, both, all, exact matches, or none (old -D"
echo " option)."
echo ""
echo " -f, --fasta_ref"
echo " type: file, file must exist"
echo " Reference fasta sequence file."
echo ""
echo " --force"
echo " type: boolean_true"
echo " Try to proceed even if malformed tags are encountered."
echo " Experimental, use at your own risk."
echo ""
echo " --keep_sum"
echo " type: string"
echo " Keep vector sum constant when splitting multiallelics (see github issue"
echo " #360)."
echo ""
echo " -m, --multiallelics"
echo " type: string"
echo " choices: [ +snps, +indels, +both, +any, -snps, -indels, -both, -any ]"
echo " Split multiallelics (-) or join biallelics (+), type: snps, indels,"
echo " both, any [default: both]."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the header."
echo ""
echo " -N, --do_not_normalize"
echo " type: boolean_true"
echo " Do not normalize indels (with -m or -c s)."
echo ""
echo " --O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " --old_rec_tag"
echo " type: string"
echo " Annotate modified records with INFO/STR indicating the original variant."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " -w, --site_win"
echo " type: integer"
echo " Buffer for sorting lines that changed position during realignment."
echo ""
echo " -s, --strict_filter"
echo " type: boolean_true"
echo " When merging (-m+), merged site is PASS only if all sites being merged"
echo " PASS."
echo ""
echo " -t, --targets"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Similar to --regions but streams rather than index-jumps."
echo ""
echo " -T, --targets_file"
echo " type: file, file must exist"
echo " Similar to --regions_file but streams rather than index-jumps."
echo ""
echo " --targets_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " Include if POS in the region (0), record overlaps (1), variant overlaps"
echo " (2)."
echo " Similar to --regions_overlap."
}
# initialise variables
VIASH_MODE='run'
@@ -589,9 +456,9 @@ 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="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:46Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -706,6 +573,165 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcftools_norm main"
echo ""
echo "Left-align and normalize indels, check if REF alleles match the reference, split"
echo "multiallelic sites into multiple rows;"
echo "recover multiallelics from multiple rows."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output normalized VCF/BCF file."
echo ""
echo "Options:"
echo " -a, --atomize"
echo " type: boolean_true"
echo " Decompose complex variants (e.g., MNVs become consecutive SNVs)."
echo ""
echo " --atom_overlaps"
echo " type: string"
echo " choices: [ ., * ]"
echo " Use the star allele (*) for overlapping alleles or set to missing (.)."
echo ""
echo " -c, --check_ref"
echo " type: string"
echo " choices: [ e, w, x, s ]"
echo " Check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad"
echo " sites."
echo ""
echo " -d, --remove_duplicates"
echo " type: string"
echo " choices: [ snps, indels, both, all, exact, none ]"
echo " Remove duplicate snps, indels, both, all, exact matches, or none (old -D"
echo " option)."
echo ""
echo " -f, --fasta_ref"
echo " type: file, file must exist"
echo " Reference fasta sequence file."
echo ""
echo " --force"
echo " type: boolean_true"
echo " Try to proceed even if malformed tags are encountered."
echo " Experimental, use at your own risk."
echo ""
echo " --keep_sum"
echo " type: string"
echo " Keep vector sum constant when splitting multiallelics (see github issue"
echo " #360)."
echo ""
echo " -m, --multiallelics"
echo " type: string"
echo " choices: [ +snps, +indels, +both, +any, -snps, -indels, -both, -any ]"
echo " Split multiallelics (-) or join biallelics (+), type: snps, indels,"
echo " both, any [default: both]."
echo ""
echo " --no_version"
echo " type: boolean_true"
echo " Do not append version and command line information to the header."
echo ""
echo " -N, --do_not_normalize"
echo " type: boolean_true"
echo " Do not normalize indels (with -m or -c s)."
echo ""
echo " --O, --output_type"
echo " type: string"
echo " choices: [ u, z, b, v ]"
echo " Output type:"
echo " u: uncompressed BCF"
echo " z: compressed VCF"
echo " b: compressed BCF"
echo " v: uncompressed VCF"
echo ""
echo " --old_rec_tag"
echo " type: string"
echo " Annotate modified records with INFO/STR indicating the original variant."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " -w, --site_win"
echo " type: integer"
echo " Buffer for sorting lines that changed position during realignment."
echo ""
echo " -s, --strict_filter"
echo " type: boolean_true"
echo " When merging (-m+), merged site is PASS only if all sites being merged"
echo " PASS."
echo ""
echo " -t, --targets"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Similar to --regions but streams rather than index-jumps."
echo ""
echo " -T, --targets_file"
echo " type: file, file must exist"
echo " Similar to --regions_file but streams rather than index-jumps."
echo ""
echo " --targets_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " Include if POS in the region (0), record overlaps (1), variant overlaps"
echo " (2)."
echo " Similar to --regions_overlap."
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=''

13
target/executable/bcftools/bcftools_sort/.config.vsh.yaml
View File

@@ -76,6 +76,9 @@ test_resources:
path: "test_data"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -184,16 +187,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_sort"
executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
viash_version: "0.9.0"
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:

86
target/executable/bcftools/bcftools_sort/bcftools_sort
View File

@@ -2,7 +2,7 @@
# bcftools_sort 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.
#
@@ -172,33 +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 "bcftools_sort main"
echo ""
echo "Sorts VCF/BCF files."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output sorted VCF/BCF file."
echo ""
echo "Options:"
echo " -O, --output_type"
echo " type: string"
echo " choices: [ b, u, z, v ]"
echo " Compresses or uncompresses the output."
echo " The options are:"
echo " b: compressed BCF,"
echo " u: uncompressed BCF,"
echo " z: compressed VCF,"
echo " v: uncompressed VCF."
}
# initialise variables
VIASH_MODE='run'
@@ -483,9 +456,9 @@ 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="2024-12-03T10:34:02Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -600,6 +573,59 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcftools_sort main"
echo ""
echo "Sorts VCF/BCF files."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, file must exist"
echo " Input VCF/BCF file."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output sorted VCF/BCF file."
echo ""
echo "Options:"
echo " -O, --output_type"
echo " type: string"
echo " choices: [ b, u, z, v ]"
echo " Compresses or uncompresses the output."
echo " The options are:"
echo " b: compressed BCF,"
echo " u: uncompressed BCF,"
echo " z: compressed VCF,"
echo " v: uncompressed VCF."
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=''

13
target/executable/bcftools/bcftools_stats/.config.vsh.yaml
View File

@@ -344,6 +344,9 @@ test_resources:
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
@@ -457,16 +460,16 @@ build_info:
engine: "docker|native"
output: "target/executable/bcftools/bcftools_stats"
executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
viash_version: "0.9.0"
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:

372
target/executable/bcftools/bcftools_stats/bcftools_stats
View File

@@ -2,7 +2,7 @@
# bcftools_stats 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.
#
@@ -172,176 +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 "bcftools_stats main"
echo ""
echo "Parses VCF or BCF and produces a txt stats file which can be plotted using"
echo "plot-vcfstats."
echo "When two files are given, the program generates separate stats for intersection"
echo "and the complements. By default only sites are compared, -s/-S must given to"
echo "include"
echo "also sample columns."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Input VCF/BCF file. Maximum of two files."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output txt statistics file."
echo ""
echo "Options:"
echo " --af_bins, --allele_frequency_bins"
echo " type: string"
echo " example: 0.1,0.5,1"
echo " Allele frequency bins, a list of bin values (0.1,0.5,1)."
echo ""
echo " --af_bins_file, --allele_frequency_bins_file"
echo " type: file, file must exist"
echo " Same as allele_frequency_bins, but in a file."
echo " Format of file is one value per line."
echo " e.g."
echo " 0.1"
echo " 0.5"
echo " 1"
echo ""
echo " --af_tag, --allele_frequency_tag"
echo " type: string"
echo " Allele frequency tag to use, by default estimated from AN,AC or GT."
echo ""
echo " --first_only, --first_allele_only"
echo " type: boolean_true"
echo " Include only 1st allele at multiallelic sites."
echo ""
echo " --c, --collapse"
echo " type: string"
echo " choices: [ snps, indels, both, all, some, none ]"
echo " Treat as identical records with <snps|indels|both|all|some|none>."
echo " See https://samtools.github.io/bcftools/bcftools.html#common_options for"
echo " details."
echo ""
echo " --d, --depth"
echo " type: string"
echo " example: 0,500,1"
echo " Depth distribution: min,max,bin size."
echo ""
echo " --e, --exclude"
echo " type: string"
echo " example: QUAL < 30 && DP < 10"
echo " Exclude sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --E, --exons"
echo " type: file, file must exist"
echo " tab-delimited file with exons for indel frameshifts statistics."
echo " The columns of the file are CHR, FROM, TO, with 1-based, inclusive,"
echo " positions."
echo " The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2"
echo " -e3 file.gz)."
echo ""
echo " --f, --apply_filters"
echo " type: string"
echo " Require at least one of the listed FILTER strings (e.g. \"PASS,.\")."
echo ""
echo " --F, --fasta_reference"
echo " type: file, file must exist"
echo " Faidx indexed reference sequence file to determine INDEL context."
echo ""
echo " --i, --include"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Select sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --I, --split_by_ID"
echo " type: boolean_true"
echo " Collect stats for sites with ID separately (known vs novel)."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " --s, --samples"
echo " type: string"
echo " List of samples for sample stats, \"-\" to include all samples."
echo ""
echo " --S, --samples_file"
echo " type: file, file must exist"
echo " File of samples to include."
echo " e.g."
echo " sample1 1"
echo " sample2 2"
echo " sample3 2"
echo ""
echo " --t, --targets"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Similar as -r, --regions, but the next position is accessed by streaming"
echo " the whole VCF/BCF"
echo " rather than using the tbi/csi index. Both -r and -t options can be"
echo " applied simultaneously: -r uses the"
echo " index to jump to a region and -t discards positions which are not in the"
echo " targets. Unlike -r, targets"
echo " can be prefixed with \"^\" to request logical complement. For example,"
echo " \"^X,Y,MT\" indicates that"
echo " sequences X, Y and MT should be skipped. Yet another difference between"
echo " the -t/-T and -r/-R is"
echo " that -r/-R checks for proper overlaps and considers both POS and the end"
echo " position of an indel,"
echo " while -t/-T considers the POS coordinate only (by default; see also"
echo " --regions-overlap and --targets-overlap)."
echo " Note that -t cannot be used in combination with -T."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --T, --targets_file"
echo " type: file, file must exist"
echo " Similar to --regions_file option but streams rather than index-jumps."
echo ""
echo " --targets_overlaps"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " Include if POS in the region (0), record overlaps (1), variant overlaps"
echo " (2)."
echo ""
echo " --u, --user_tstv"
echo " type: string"
echo " Collect Ts/Tv stats for any tag using the given binning [0:1:100]."
echo " Format is <TAG[:min:max:n]>."
echo " A subfield can be selected as e.g. 'PV4[0]', here the first value of the"
echo " PV4 tag."
echo ""
echo " --v, --verbose"
echo " type: boolean_true"
echo " Produce verbose per-site and per-sample output."
}
# initialise variables
VIASH_MODE='run'
@@ -626,9 +456,9 @@ 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="2024-12-03T10:34:03Z"
LABEL org.opencontainers.image.created="2025-03-06T09:19:35Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
LABEL org.opencontainers.image.revision="5f6516e9c0d95c84f3d4159a67d3de19d3ae1fde"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -743,6 +573,202 @@ fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "bcftools_stats main"
echo ""
echo "Parses VCF or BCF and produces a txt stats file which can be plotted using"
echo "plot-vcfstats."
echo "When two files are given, the program generates separate stats for intersection"
echo "and the complements. By default only sites are compared, -s/-S must given to"
echo "include"
echo "also sample columns."
echo ""
echo "Inputs:"
echo " -i, --input"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " Input VCF/BCF file. Maximum of two files."
echo ""
echo "Outputs:"
echo " -o, --output"
echo " type: file, required parameter, output, file must exist"
echo " Output txt statistics file."
echo ""
echo "Options:"
echo " --af_bins, --allele_frequency_bins"
echo " type: string"
echo " example: 0.1,0.5,1"
echo " Allele frequency bins, a list of bin values (0.1,0.5,1)."
echo ""
echo " --af_bins_file, --allele_frequency_bins_file"
echo " type: file, file must exist"
echo " Same as allele_frequency_bins, but in a file."
echo " Format of file is one value per line."
echo " e.g."
echo " 0.1"
echo " 0.5"
echo " 1"
echo ""
echo " --af_tag, --allele_frequency_tag"
echo " type: string"
echo " Allele frequency tag to use, by default estimated from AN,AC or GT."
echo ""
echo " --first_only, --first_allele_only"
echo " type: boolean_true"
echo " Include only 1st allele at multiallelic sites."
echo ""
echo " --c, --collapse"
echo " type: string"
echo " choices: [ snps, indels, both, all, some, none ]"
echo " Treat as identical records with <snps|indels|both|all|some|none>."
echo " See https://samtools.github.io/bcftools/bcftools.html#common_options for"
echo " details."
echo ""
echo " --d, --depth"
echo " type: string"
echo " example: 0,500,1"
echo " Depth distribution: min,max,bin size."
echo ""
echo " --e, --exclude"
echo " type: string"
echo " example: QUAL < 30 && DP < 10"
echo " Exclude sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --E, --exons"
echo " type: file, file must exist"
echo " tab-delimited file with exons for indel frameshifts statistics."
echo " The columns of the file are CHR, FROM, TO, with 1-based, inclusive,"
echo " positions."
echo " The file is BGZF-compressed and indexed with tabix (e.g. tabix -s1 -b2"
echo " -e3 file.gz)."
echo ""
echo " --f, --apply_filters"
echo " type: string"
echo " Require at least one of the listed FILTER strings (e.g. \"PASS,.\")."
echo ""
echo " --F, --fasta_reference"
echo " type: file, file must exist"
echo " Faidx indexed reference sequence file to determine INDEL context."
echo ""
echo " --i, --include"
echo " type: string"
echo " example: QUAL >= 30 && DP >= 10"
echo " Select sites for which the expression is true."
echo " See https://samtools.github.io/bcftools/bcftools.html#expressions for"
echo " details."
echo ""
echo " --I, --split_by_ID"
echo " type: boolean_true"
echo " Collect stats for sites with ID separately (known vs novel)."
echo ""
echo " --r, --regions"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Restrict to comma-separated list of regions."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --R, --regions_file"
echo " type: file, file must exist"
echo " Restrict to regions listed in a file."
echo " Regions can be specified either on a VCF, BED, or tab-delimited file"
echo " (the default)."
echo " For more information check manual."
echo ""
echo " --regions_overlap"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " This option controls how overlapping records are determined:"
echo " set to 'pos' or '0' if the VCF record has to have POS inside a region"
echo " (this corresponds to the default behavior of -t/-T);"
echo " set to 'record' or '1' if also overlapping records with POS outside a"
echo " region should be included (this is the default behavior of -r/-R,"
echo " and includes indels with POS at the end of a region, which are"
echo " technically outside the region);"
echo " or set to 'variant' or '2' to include only true overlapping variation"
echo " (compare the full VCF representation \"TA>T-\" vs the true sequence"
echo " variation \"A>-\")."
echo ""
echo " --s, --samples"
echo " type: string"
echo " List of samples for sample stats, \"-\" to include all samples."
echo ""
echo " --S, --samples_file"
echo " type: file, file must exist"
echo " File of samples to include."
echo " e.g."
echo " sample1 1"
echo " sample2 2"
echo " sample3 2"
echo ""
echo " --t, --targets"
echo " type: string"
echo " example: 20:1000000-2000000"
echo " Similar as -r, --regions, but the next position is accessed by streaming"
echo " the whole VCF/BCF"
echo " rather than using the tbi/csi index. Both -r and -t options can be"
echo " applied simultaneously: -r uses the"
echo " index to jump to a region and -t discards positions which are not in the"
echo " targets. Unlike -r, targets"
echo " can be prefixed with \"^\" to request logical complement. For example,"
echo " \"^X,Y,MT\" indicates that"
echo " sequences X, Y and MT should be skipped. Yet another difference between"
echo " the -t/-T and -r/-R is"
echo " that -r/-R checks for proper overlaps and considers both POS and the end"
echo " position of an indel,"
echo " while -t/-T considers the POS coordinate only (by default; see also"
echo " --regions-overlap and --targets-overlap)."
echo " Note that -t cannot be used in combination with -T."
echo " Following formats are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​]."
echo ""
echo " --T, --targets_file"
echo " type: file, file must exist"
echo " Similar to --regions_file option but streams rather than index-jumps."
echo ""
echo " --targets_overlaps"
echo " type: string"
echo " choices: [ pos, record, variant, 0, 1, 2 ]"
echo " Include if POS in the region (0), record overlaps (1), variant overlaps"
echo " (2)."
echo ""
echo " --u, --user_tstv"
echo " type: string"
echo " Collect Ts/Tv stats for any tag using the given binning [0:1:100]."
echo " Format is <TAG[:min:max:n]>."
echo " A subfield can be selected as e.g. 'PV4[0]', here the first value of the"
echo " PV4 tag."
echo ""
echo " --v, --verbose"
echo " type: boolean_true"
echo " Produce verbose per-site and per-sample output."
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=''