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biobox/target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
CI a7b0d33a32 Build branch main with version main (aa43543) 
Build pipeline: viash-hub.biobox.main-2k68h

Source commit: aa43543e1f

Source message: Rseqc innerdistance (#159)

* initial commit dedup

* Revert "initial commit dedup"

This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.

* full component with two tests

* fix default values

* adjust argument names and container image

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
2024-10-26 19:02:37 +00:00

497 lines
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YAML
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name: "bcftools_annotate"
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"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatician"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
alternatives:
- "-i"
description: "Input VCF/BCF file."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "-o"
description: "Output annotated file."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- name: "Options"
description: "For examples on how to use use bcftools annotate see http://samtools.github.io/bcftools/howtos/annotate.html.\n\
For more details on the options see https://samtools.github.io/bcftools/bcftools.html#annotate.\n"
arguments:
- type: "file"
name: "--annotations"
alternatives:
- "--a"
description: "VCF file or tabix-indexed FILE with annotations: CHR\\tPOS[\\tVALUE]+\
\ . \n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--columns"
alternatives:
- "--c"
description: "List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG.\
\ \nSee man page for details.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--columns_file"
alternatives:
- "--C"
description: "Read -c columns from FILE, one name per row, with optional --merge_logic\
\ TYPE: NAME[ TYPE].\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--exclude"
alternatives:
- "--e"
description: "Exclude sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL >= 30 && DP >= 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--force"
description: "continue even when parsing errors, such as undefined tags, are encountered.\
\ \nNote this can be an unsafe operation and can result in corrupted BCF files.\
\ \nIf this option is used, make sure to sanity check the result thoroughly.\n"
info: null
direction: "input"
- type: "string"
name: "--header_line"
alternatives:
- "--H"
description: "Header line which should be appended to the VCF header, can be given\
\ multiple times.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--header_lines"
alternatives:
- "--h"
description: "File with header lines to append to the VCF header.\nFor example:\n\
\ ##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description=\"Example header\
\ line\">\n ##INFO=<ID=STRING_TAG,Number=1,Type=String,Description=\"Yet another\
\ header line\">\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--set_id"
alternatives:
- "--I"
description: "Set ID column using a `bcftools query`-like expression, see man\
\ page for details.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--include"
description: "Select sites for which the expression is true.\nSee https://samtools.github.io/bcftools/bcftools.html#expressions\
\ for details.\n"
info: null
example:
- "QUAL >= 30 && DP >= 10"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--keep_sites"
alternatives:
- "--k"
description: "Leave --include/--exclude sites unchanged instead of discarding\
\ them.\n"
info: null
direction: "input"
- type: "string"
name: "--merge_logic"
alternatives:
- "--l"
description: "When multiple regions overlap a single record, this option defines\
\ how to treat multiple annotation values.\nSee man page for more details.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--mark_sites"
alternatives:
- "--m"
description: "Annotate sites which are present (\"+\") or absent (\"-\") in the\
\ -a file with a new INFO/TAG flag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--min_overlap"
description: "Minimum overlap required as a fraction of the variant in the annotation\
\ -a file (ANN), \nin the target VCF file (:VCF), or both for reciprocal overlap\
\ (ANN:VCF). \nBy default overlaps of arbitrary length are sufficient. \nThe\
\ option can be used only with the tab-delimited annotation -a file and with\
\ BEG and END columns present.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--no_version"
description: "Do not append version and command line information to the output\
\ VCF header.\n"
info: null
direction: "input"
- type: "string"
name: "--output_type"
alternatives:
- "--O"
description: "Output type:\n u: uncompressed BCF\n z: compressed VCF\n b: compressed\
\ BCF\n v: uncompressed VCF\n"
info: null
required: false
choices:
- "u"
- "z"
- "b"
- "v"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--pair_logic"
description: "Controls how to match records from the annotation file to the target\
\ VCF. \nEffective only when -a is a VCF or BCF file. \nThe option replaces\
\ the former uninuitive --collapse. \nSee Common Options for more.\n"
info: null
required: false
choices:
- "snps"
- "indels"
- "both"
- "all"
- "some"
- "exact"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions"
alternatives:
- "--r"
description: "Restrict to comma-separated list of regions. \nFollowing formats\
\ are supported: chr|chr:pos|chr:beg-end|chr:beg-[,…​].\n"
info: null
example:
- "20:1000000-2000000"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--regions_file"
alternatives:
- "--R"
description: "Restrict to regions listed in a file. \nRegions can be specified\
\ either on a VCF, BED, or tab-delimited file (the default). \nFor more information\
\ check manual.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--regions_overlap"
description: "This option controls how overlapping records are determined: \n\
set to 'pos' or '0' if the VCF record has to have POS inside a region (this\
\ corresponds to the default behavior of -t/-T); \nset to 'record' or '1' if\
\ also overlapping records with POS outside a region should be included (this\
\ is the default behavior of -r/-R, \nand includes indels with POS at the end\
\ of a region, which are technically outside the region); \nor set to 'variant'\
\ or '2' to include only true overlapping variation (compare the full VCF representation\
\ \"TA>T-\" vs the true sequence variation \"A>-\").\n"
info: null
required: false
choices:
- "pos"
- "record"
- "variant"
- "0"
- "1"
- "2"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rename_annotations"
description: "Rename annotations: TYPE/old\\tnew, where TYPE is one of FILTER,INFO,FORMAT.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rename_chromosomes"
description: "Rename chromosomes according to the map in file, with \"old_name\
\ new_name\\n\" pairs \nseparated by whitespaces, each on a separate line.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--samples"
description: "Subset of samples to annotate.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--samples_file"
description: "Subset of samples to annotate in file format.\nSee also https://samtools.github.io/bcftools/bcftools.html#common_options.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--single_overlaps"
description: "Use this option to keep memory requirements low with very large\
\ annotation files. \nNote, however, that this comes at a cost, only single\
\ overlapping intervals are considered in this mode. \nThis was the default\
\ mode until the commit af6f0c9 (Feb 24 2019).\n"
info: null
direction: "input"
- type: "string"
name: "--remove"
alternatives:
- "--x"
description: "List of annotations to remove. \nUse \"FILTER\" to remove all filters\
\ or \"FILTER/SomeFilter\" to remove a specific filter. \nSimilarly, \"INFO\"\
\ can be used to remove all INFO tags and \"FORMAT\" to remove all FORMAT tags\
\ except GT. \nTo remove all INFO tags except \"FOO\" and \"BAR\", use \"^INFO/FOO,INFO/BAR\"\
\ (and similarly for FORMAT and FILTER). \n\"INFO\" can be abbreviated to \"\
INF\" and \"FORMAT\" to \"FMT\".\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Add or remove annotations from a VCF/BCF file.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "Annotate"
- "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#annotate"
issue_tracker: "https://github.com/samtools/bcftools/issues"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "debian:stable-slim"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "bcftools"
- "procps"
interactive: false
- type: "docker"
run:
- "echo \"bcftools: \\\"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftools\
\ //p')\\\"\" > /var/software_versions.txt\n"
test_setup:
- type: "apt"
packages:
- "tabix"
interactive: false
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/bcftools/bcftools_annotate/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/bcftools/bcftools_annotate"
executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
viash_version: "0.9.0"
git_commit: "aa43543e1fb609901d09b7a9f0c5e72707cb47a4"
git_remote: "https://x-access-token:ghs_9v4VhFt3rgNHA8iZY5HYB5rN6bmxTd2UtBuO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-20-gaa43543"
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"
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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