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

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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 `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
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- vcfs:
type: files
description: |
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List containing 2 or more vcf files
e.g. [ 'file1.vcf', 'file2.vcf' ]
- tbis:
type: files
description: |
List containing the tbi index files corresponding to the vcfs input files
e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
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output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
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- results:
type: directory
description: Folder containing the set operations results perform on the vcf files
pattern: "${prefix}"
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- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"