mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
61 lines
1.7 KiB
YAML
61 lines
1.7 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
|
|
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"
|