nf-core_modules/modules/gatk4/createsomaticpanelofnormals/meta.yml

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name: gatk4_createsomaticpanelofnormals
description: Create a panel of normals contraining germline and artifactual sites for use with mutect2.
keywords:
- gatk4
- createsomaticpanelofnormals
- panelofnormals
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']
- genoomicsdb:
type: directory
description: genomicsDB workspace that contains the samples to create the somatic panel of normals with.
pattern: "*_genomicsDBworkspace"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
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- fai:
type: file
description: Index of reference fasta file
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pattern: "*.fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: "*.dict"
output:
- vcf:
type: file
description: panel of normal as compressed vcf file
pattern: "*.vcf.gz"
- tbi:
type: file
description: Tabix index of vcf file
pattern: "*vcf.gz.tbi"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@GCJMackenzie"