nf-core_modules/software/bcftools/isec/meta.yml

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YAML

name: bcftools_isec
description: Apply set operations to VCF files
keywords:
- variant calling
- intersect
- union
- complement
- VCF
tools:
- isec:
description: |
Computes intersections, unions and complements of VCF files.
homepage: http://samtools.github.io/bcftools/bcftools.html
documentation: http://www.htslib.org/doc/bcftools.html
doi: 10.1093/bioinformatics/btp352
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: files
description: |
List containing 2 or more vcf files and their respective index (tbi files)
e.g. [ 'file1.vcf', 'file1.vcf.tbi', 'file2.vcf', 'file2.vcf.tbi' ]
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf:
type: file
description: VCF filtered output file
pattern: "*.{vcf}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"