mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
c5634ba99b
* initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
62 lines
1.8 KiB
YAML
62 lines
1.8 KiB
YAML
name: bcftools_view
|
|
description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
|
keywords:
|
|
- variant calling
|
|
- view
|
|
- bcftools
|
|
- VCF
|
|
|
|
tools:
|
|
- view:
|
|
description: |
|
|
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
|
|
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 inspected.
|
|
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 normalized output file
|
|
pattern: "*.{vcf.gz}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@abhi18av"
|