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biobox/target/executable/bcftools/bcftools_norm/.config.vsh.yaml
CI 27d6133895 Build branch biobox/main with version main to biobox on branch main (9991e9a) 
Build pipeline: viash-hub.biobox.main-l6hlj

Source commit: 9991e9a4f5

Source message: Bump bases2fastq to 2.2.1 (#202)
2025-10-03 08:31:27 +00:00

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name: "bcftools_norm"
namespace: "bcftools"
version: "main"
authors:
- name: "Theodoro Gasperin Terra Camargo"
roles:
- "author"
info:
links:
email: "theodorogtc@gmail.com"
github: "tgaspe"
linkedin: "theodoro-gasperin-terra-camargo"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
description: "Input VCF/BCF file.\n\nThe file to be normalized, left-aligned,\
\ and/or processed.\n"
info: null
example:
- "input.vcf.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Write output to a file.\n\nIf not specified, output goes to standard\
\ output.\n"
info: null
example:
- "normalized.vcf.gz"
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Options"
arguments:
- type: "boolean_true"
name: "--atomize"
alternatives:
- "-a"
description: "Decompose complex variants (e.g., MNVs become consecutive SNVs).\n\
\nBreaks down complex variants into simpler components.\n"
info: null
direction: "input"
- type: "string"
name: "--atom_overlaps"
description: "Use the star allele (*) for overlapping alleles or set to missing\
\ (.).\n\n**Options:**\n- `*`: Use star allele for overlaps (default)\n- `.`:\
\ Set overlapping alleles to missing\n"
info: null
example:
- "*"
required: false
choices:
- "."
- "*"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--check_ref"
alternatives:
- "-c"
description: "Check REF alleles and exit (e), warn (w), exclude (x), or set (s)\
\ bad sites.\n\n**Options:**\n- `e`: exit on REF mismatch (default)\n- `w`:\
\ warn about REF mismatches\n- `x`: exclude sites with REF mismatches\n- `s`:\
\ set/fix REF mismatches\n"
info: null
example:
- "w"
required: false
choices:
- "e"
- "w"
- "x"
- "s"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--remove_duplicates_flag"
alternatives:
- "-D"
description: "Remove duplicate lines of the same type.\n\nShorthand for --rm_dup\
\ exact.\n"
info: null
direction: "input"
- type: "string"
name: "--rm_dup"
alternatives:
- "-d"
description: "Remove duplicate snps|indels|both|all|exact.\n\n**Options:**\n-\
\ `snps`: Remove duplicate SNPs\n- `indels`: Remove duplicate indels\n- `both`:\
\ Remove duplicate SNPs and indels\n- `all`: Remove all duplicates\n- `exact`:\
\ Remove exact duplicates only\n"
info: null
example:
- "exact"
required: false
choices:
- "snps"
- "indels"
- "both"
- "all"
- "exact"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--exclude"
alternatives:
- "-e"
description: "Do not normalize records for which the expression is true.\n\nUses\
\ bcftools expression syntax (see man page for details).\n"
info: null
example:
- "INFO/DP<10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fasta_ref"
alternatives:
- "-f"
description: "Reference sequence file.\n\nRequired for checking REF alleles and\
\ left-alignment.\n"
info: null
example:
- "reference.fa"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--force"
description: "Try to proceed even if malformed tags are encountered.\n\n**Warning:**\
\ Experimental feature, use at your own risk.\n"
info: null
direction: "input"
- type: "file"
name: "--gff_annot"
alternatives:
- "-g"
description: "Follow HGVS 3'rule and right-align variants in transcripts on the\
\ forward strand.\n\nUses GFF annotation file for transcript information.\n"
info: null
example:
- "genes.gff"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--include"
alternatives:
- "-i"
description: "Normalize only records for which the expression is true.\n\nUses\
\ bcftools expression syntax (see man page for details).\n"
info: null
example:
- "QUAL>=30"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--keep_sum"
description: "Keep vector sum constant when splitting multiallelics.\n\nComma-separated\
\ list of INFO tags (see github issue #360).\n"
info: null
example:
- "AC,AF"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--multiallelics"
alternatives:
- "-m"
description: "Split multiallelics (-) or join biallelics (+), type: snps|indels|both|any.\n\
\n**Options:**\n- `-both`: Split multiallelic sites (default)\n- `+both`: Join\
\ biallelic sites\n- Use `snps`, `indels`, `any` for specific variant types\n"
info: null
example:
- "-both"
required: false
choices:
- "+snps"
- "+indels"
- "+both"
- "+any"
- "-snps"
- "-indels"
- "-both"
- "-any"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--multi_overlaps"
description: "Fill in the reference (0) or missing (.) allele when splitting multiallelics.\n\
\n**Options:**\n- `0`: Fill with reference allele (default)\n- `.`: Fill with\
\ missing allele\n"
info: null
example:
- "0"
required: false
choices:
- "0"
- "."
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--no_version"
description: "Do not append version and command line to the header.\n\nProduces\
\ cleaner output headers.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--do_not_normalize"
alternatives:
- "-N"
description: "Do not normalize indels (with -m or -c s).\n\nSkips indel left-alignment\
\ and normalization.\n"
info: null
direction: "input"
- type: "string"
name: "--old_rec_tag"
description: "Annotate modified records with INFO/STR indicating the original\
\ variant.\n\nAdds specified INFO tag to track original variants.\n"
info: null
example:
- "OLD_VARIANT"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--output_type"
alternatives:
- "-O"
description: "Output type and compression level.\n\n**Options:**\n- `u`: uncompressed\
\ BCF\n- `b`: compressed BCF\n- `v`: uncompressed VCF (default)\n- `z`: compressed\
\ VCF (with optional compression level 0-9)\n"
info: null
example:
- "z"
required: false
choices:
- "u"
- "z"
- "b"
- "v"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions"
alternatives:
- "-r"
description: "Restrict to comma-separated list of regions.\n\n**Formats supported:**\
\ chr|chr:pos|chr:beg-end|chr:beg-[,…​]\n"
info: null
example:
- "chr20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--regions_file"
alternatives:
- "-R"
description: "Restrict to regions listed in a file.\n\nRegions can be specified\
\ in VCF, BED, or tab-delimited format.\n"
info: null
example:
- "regions.bed"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions_overlap"
description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
\ (2).\n\n**Options:**\n- `0`: POS inside region (default for -t/-T)\n- `1`:\
\ overlapping records included (default for -r/-R)\n- `2`: true overlapping\
\ variation only\n"
info: null
example:
- "1"
required: false
choices:
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--strict_filter"
alternatives:
- "-s"
description: "When merging (-m+), merged site is PASS only if all sites being\
\ merged PASS.\n\nStricter FILTER handling during multiallelic joining.\n"
info: null
direction: "input"
- type: "string"
name: "--sort"
alternatives:
- "-S"
description: "Sort order: chr_pos,lex.\n\n**Options:**\n- `chr_pos`: Sort by chromosome\
\ and position (default)\n- `lex`: Lexicographic sort\n"
info: null
example:
- "chr_pos"
required: false
choices:
- "chr_pos"
- "lex"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets"
alternatives:
- "-t"
description: "Similar to --regions but streams rather than index-jumps.\n\nMore\
\ efficient for processing many small regions.\n"
info: null
example:
- "chr20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--targets_file"
alternatives:
- "-T"
description: "Similar to --regions_file but streams rather than index-jumps.\n\
\nMore efficient for processing many regions from file.\n"
info: null
example:
- "targets.bed"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--targets_overlap"
description: "Include if POS in the region (0), record overlaps (1), variant overlaps\
\ (2).\n\nSimilar to --regions_overlap but for streaming mode.\n"
info: null
example:
- "0"
required: false
choices:
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--verbosity"
alternatives:
- "-v"
description: "Verbosity level.\n\nControls amount of diagnostic output.\n"
info: null
example:
- 1
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--site_win"
alternatives:
- "-w"
description: "Buffer for sorting lines which changed position during realignment.\n\
\nLarger values use more memory but handle more complex rearrangements.\n"
info: null
example:
- 1000
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--write_index"
alternatives:
- "-W"
description: "Automatically index the output files.\n\n**Format:** Specify index\
\ format or use default.\n"
info: null
example:
- "tbi"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Left-align and normalize indels, check if REF alleles match the reference,\
\ split multiallelic sites into multiple rows; \nrecover multiallelics from multiple\
\ rows. \n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_helpers.sh"
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "bcftools"
- "ps"
keywords:
- "Normalize"
- "VCF"
- "BCF"
license: "MIT/Expat, GNU"
references:
doi:
- "https://doi.org/10.1093/gigascience/giab008"
links:
repository: "https://github.com/samtools/bcftools"
homepage: "https://samtools.github.io/bcftools/"
documentation: "https://samtools.github.io/bcftools/bcftools.html#norm"
issue_tracker: "https://github.com/samtools/bcftools/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/bcftools:1.22--h3a4d415_1"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "bcftools --version 2>&1 | head -1 | sed 's/bcftools /bcftools: /' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/bcftools/bcftools_norm/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/bcftools/bcftools_norm"
executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
viash_version: "0.9.4"
git_commit: "9991e9a4f5ddd5085a4e2becf962950b1daf594b"
git_remote: "https://github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "main"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"
target: "target"
config_mods:
- ".requirements.commands += ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"
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