CI
6f2f840fd9
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e
Source message: BD rhapsody sequence analysis (#96)
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
363 lines
10 KiB
YAML
363 lines
10 KiB
YAML
name: "bcftools_concat"
|
|
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 files to concatenate."
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: false
|
|
direction: "input"
|
|
multiple: true
|
|
multiple_sep: ";"
|
|
- type: "file"
|
|
name: "--file_list"
|
|
alternatives:
|
|
- "-f"
|
|
description: "Read the list of VCF/BCF files from a file, one file name per line."
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: false
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- name: "Outputs"
|
|
arguments:
|
|
- type: "file"
|
|
name: "--output"
|
|
alternatives:
|
|
- "-o"
|
|
description: "Output concatenated VCF/BCF file."
|
|
info: null
|
|
must_exist: true
|
|
create_parent: true
|
|
required: true
|
|
direction: "output"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- name: "Options"
|
|
arguments:
|
|
- type: "boolean_true"
|
|
name: "--allow_overlaps"
|
|
alternatives:
|
|
- "-a"
|
|
description: "First coordinate of the next file can precede last record of the\
|
|
\ current file.\n"
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--compact_PS"
|
|
alternatives:
|
|
- "-c"
|
|
description: "Do not output PS tag at each site, only at the start of a new phase\
|
|
\ set block.\n"
|
|
info: null
|
|
direction: "input"
|
|
- type: "string"
|
|
name: "--remove_duplicates"
|
|
alternatives:
|
|
- "-d"
|
|
description: "Output duplicate records present in multiple files only once: <snps|indels|both|all|exact>.\n\
|
|
\ \n"
|
|
info: null
|
|
required: false
|
|
choices:
|
|
- "snps"
|
|
- "indels"
|
|
- "both"
|
|
- "all"
|
|
- "exact"
|
|
- "none"
|
|
direction: "input"
|
|
multiple: false
|
|
multiple_sep: ";"
|
|
- type: "boolean_true"
|
|
name: "--ligate"
|
|
alternatives:
|
|
- "-l"
|
|
description: "Ligate phased VCFs by matching phase at overlapping haplotypes."
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--ligate_force"
|
|
description: "Ligate even non-overlapping chunks, keep all sites."
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--ligate_warn"
|
|
description: "Drop sites in imperfect overlaps."
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--no_version"
|
|
description: "Do not append version and command line information to the header."
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--naive"
|
|
alternatives:
|
|
- "-n"
|
|
description: "Concatenate files without recompression, a header check compatibility\
|
|
\ is performed."
|
|
info: null
|
|
direction: "input"
|
|
- type: "boolean_true"
|
|
name: "--naive_force"
|
|
description: "Same as --naive, but header compatibility is not checked. \nDangerous,\
|
|
\ use with caution.\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: "integer"
|
|
name: "--min_PQ"
|
|
alternatives:
|
|
- "-q"
|
|
description: "Break phase set if phasing quality is lower than <int>."
|
|
info: null
|
|
example:
|
|
- 30
|
|
required: false
|
|
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: ";"
|
|
resources:
|
|
- type: "bash_script"
|
|
path: "script.sh"
|
|
is_executable: true
|
|
description: "Concatenate or combine VCF/BCF files. All source files must have the\
|
|
\ same sample\ncolumns appearing in the same order. The program can be used, for\
|
|
\ example, to\nconcatenate chromosome VCFs into one VCF, or combine a SNP VCF and\
|
|
\ an indel\nVCF into one. The input files must be sorted by chr and position. The\
|
|
\ files\nmust be given in the correct order to produce sorted VCF on output unless\n\
|
|
the -a, --allow-overlaps option is specified. With the --naive option, the files\n\
|
|
are concatenated without being recompressed, which is very fast.\n"
|
|
test_resources:
|
|
- type: "bash_script"
|
|
path: "test.sh"
|
|
is_executable: true
|
|
info: null
|
|
status: "enabled"
|
|
requirements:
|
|
commands:
|
|
- "ps"
|
|
keywords:
|
|
- "Concatenate"
|
|
- "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#concat"
|
|
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_concat/config.vsh.yaml"
|
|
runner: "executable"
|
|
engine: "docker|native"
|
|
output: "target/executable/bcftools/bcftools_concat"
|
|
executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
|
|
viash_version: "0.9.0"
|
|
git_commit: "7f8bcc2b3e1ffaac9778b6acb42420b19660d1a1"
|
|
git_remote: "https://x-access-token:ghs_aSDBedV4vU66pddFDN6d8UEy0ZQApn08RAsh@github.com/viash-hub/biobox"
|
|
git_tag: "v0.2.0-3-g7f8bcc2"
|
|
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"
|