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meta.yml
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meta.yml
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name: "gatk4_filtervarianttranches"
description: Apply tranche filtering
keywords:
- filtervarianttranches
- gatk4
- tranche filtering
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/articles/360051308071-FilterVariantTranches
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', single_end:false ]
- vcf:
type: file
description: a VCF file containing variants, must have info key:CNN_2D
pattern: "*.vcf.gz"
- tbi:
type: file
description: tbi file matching with -vcf
pattern: "*.vcf.gz.tbi"
- resources:
type: list
description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
pattern: "*.vcf.gz"
- resources_index:
type: list
description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
pattern: "*.vcf.gz"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
- fai:
type: file
description: Index of reference fasta file
pattern: "fasta.fai"
- dict:
type: file
description: GATK sequence dictionary
pattern: ".dict"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf:
type: file
description: VCF file
pattern: "*.vcf.gz"
- tbi:
type: file
description: VCF index file
pattern: "*.vcf.gz.tbi"
authors:
- "@FriederikeHanssen"
maintainers:
- "@FriederikeHanssen"