mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
43a1c1c6d1
* Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
56 lines
1.6 KiB
YAML
56 lines
1.6 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
|
|
licence: ['Apache-2.0']
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test']
|
|
- vcf:
|
|
type: list
|
|
description: List of VCF(.gz) files
|
|
pattern: "*.{vcf,vcf.gz}"
|
|
- vcf_tbi:
|
|
type: list
|
|
description: List of VCF file indexes
|
|
pattern: "*.{idx,tbi}"
|
|
- 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: Compressed VCF file
|
|
pattern: "*.vcf.gz"
|
|
- tbi:
|
|
type: file
|
|
description: Index of VCF file
|
|
pattern: "*.vcf.gz.tbi"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@kevinmenden"
|