mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
67 lines
2 KiB
YAML
67 lines
2 KiB
YAML
name: bcftools_merge
|
|
description: Merge VCF files
|
|
keywords:
|
|
- variant calling
|
|
- merge
|
|
- VCF
|
|
tools:
|
|
- merge:
|
|
description: |
|
|
Merge 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 ]
|
|
- vcfs:
|
|
type: files
|
|
description: |
|
|
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' ]
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- vcf:
|
|
type: file
|
|
description: VCF merged output file
|
|
pattern: "*.{vcf.gz}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@joseespinosa"
|
|
- "@drpatelh"
|