2021-02-19 12:29:08 +00:00
|
|
|
name: gatk4_mergevcfs
|
|
|
|
|
description: Merges several vcf files
|
|
|
|
|
keywords:
|
|
|
|
|
- vcf
|
|
|
|
|
- merge
|
|
|
|
|
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
|
|
|
|
|
input:
|
|
|
|
|
- meta:
|
|
|
|
|
type: map
|
|
|
|
|
description: |
|
|
|
|
|
Groovy Map containing sample information
|
|
|
|
|
e.g. [ id:'test']
|
2021-02-22 14:10:20 +00:00
|
|
|
- vcf:
|
2021-02-19 12:29:08 +00:00
|
|
|
type: list
|
|
|
|
|
description: Two or more VCF files
|
|
|
|
|
pattern: "*.{vcf,vcf.gz}"
|
2021-02-19 13:09:32 +00:00
|
|
|
- ref_dict:
|
|
|
|
|
type: file
|
|
|
|
|
description: Optional Sequence Dictionary as input
|
|
|
|
|
pattern: "*.dict"
|
|
|
|
|
- use_ref_dict:
|
|
|
|
|
type: boolean
|
|
|
|
|
description: Specify whether or not to use a given reference dictionary
|
2021-02-19 12:29:08 +00:00
|
|
|
output:
|
|
|
|
|
- vcf:
|
|
|
|
|
type: file
|
|
|
|
|
description: merged vcf file
|
|
|
|
|
pattern: "*.vcf.gz"
|
|
|
|
|
- version:
|
|
|
|
|
type: file
|
|
|
|
|
description: File containing software version
|
|
|
|
|
pattern: "*.version.txt"
|
|
|
|
|
authors:
|
|
|
|
|
- "@kevinmenden"
|
