mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
17dbff52f4
* added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
68 lines
2.1 KiB
YAML
68 lines
2.1 KiB
YAML
name: gatk4_variantfiltration
|
|
description: Filter variants
|
|
keywords:
|
|
- vcf
|
|
- filter
|
|
tools:
|
|
- gatk4:
|
|
description: |
|
|
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
|
|
with a primary focus on variant discovery and genotyping. Its powerful processing engine
|
|
and high-performance computing features make it capable of taking on projects of any size.
|
|
homepage: https://gatk.broadinstitute.org/hc/en-us
|
|
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
|
|
doi: 10.1158/1538-7445.AM2017-3590
|
|
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']
|
|
- vcf:
|
|
type: list
|
|
description: Input VCF file
|
|
pattern: "*.{vcf}"
|
|
- fasta:
|
|
type: file
|
|
description: Fasta file of reference genome
|
|
pattern: "*.fasta"
|
|
- fai:
|
|
type: file
|
|
description: Index of fasta file
|
|
pattern: "*.fasta.fai"
|
|
- dict:
|
|
type: file
|
|
description: Sequence dictionary of fastea file
|
|
pattern: "*.dict"
|
|
output:
|
|
- vcf:
|
|
type: file
|
|
description: filtered VCF file
|
|
pattern: "*.filtered.{vcf}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.version.txt"
|
|
authors:
|
|
- "@kevinmenden"
|