nf-core_modules/modules/bcftools/query/meta.yml
Abhinav Sharma 6ff995e93d
Add bcftools/query module (#670)
* initial commit [ci skip]

* add basic structure [ci skip]

* finalized the bcftools/query module

* add optional files [ci skip]

* Add the vcf index file as param [ci skip]

* update the md5sum for output file [ci skip]

* all tests passing
2021-09-14 09:19:01 +02:00

61 lines
1.8 KiB
YAML

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
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.
e.g. 'file.vcf'
- index:
type: file
description: |
The tab index for the VCF file to be inspected.
e.g. 'file.tbi'
- regions:
type: file
description: |
Optionally, restrict the operation to regions listed in this file.
e.g. 'file.vcf'
- targets:
type: file
description: |
Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
e.g. 'file.vcf'
- 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 ]
- vcf:
type: file
description: VCF query output file
pattern: "*.{vcf.gz}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@abhi18av"