nf-core_modules/modules/bcftools/query/meta.yml

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name: bcftools_query
description: Extracts fields from VCF or BCF files and outputs them in user-defined format.
keywords:
- query
- variant calling
- bcftools
- VCF
tools:
- query:
description: |
Extracts fields from VCF or BCF files and outputs them in user-defined format.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: |
The vcf file to be qeuried.
pattern: "*.{vcf.gz, vcf}"
- tbi:
type: file
description: |
The tab index for the VCF file to be inspected.
pattern: "*.tbi"
- regions:
type: file
description: |
Optionally, restrict the operation to regions listed in this file.
- targets:
type: file
description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
- samples:
type: file
description: |
Optional, file of sample names to be included or excluded.
e.g. 'file.tsv'
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- txt:
type: file
description: BCFTools query output file
pattern: "*.txt"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@abhi18av"
- "@drpatelh"