nf-core_modules/modules/gatk/indelrealigner/meta.yml
2022-06-09 08:26:04 +02:00

71 lines
2 KiB
YAML

name: "gatk_indelrealigner"
description: Performs local realignment around indels to correct for mapping errors
keywords:
- bam
- vcf
- variant calling
- indel
- realignment
tools:
- "gatk":
description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
homepage: "https://gatk.broadinstitute.org/hc/en-us"
documentation: "https://github.com/broadinstitute/gatk-docs"
licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: Sorted and indexed BAM file
pattern: "*.bam"
- bai:
type: file
description: BAM index file
pattern: "*.bai"
- intervals:
type: file
description: Intervals file created by gatk3 RealignerTargetCreator
pattern: "*.{intervals,list}"
- fasta:
type: file
description: Reference file used to generate BAM file
pattern: ".{fasta,fa,fna}"
- fai:
type: file
description: Index of reference file used to generate BAM file
pattern: ".fai"
- dict:
type: file
description: GATK dict file for reference
pattern: ".dict"
- known_vcf:
type: file
description: Optional input VCF file(s) with known indels
pattern: ".vcf"
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"
- bam:
type: file
description: Sorted and indexed BAM file with local realignment around variants
pattern: "*.bam"
- bai:
type: file
description: Output BAM Index file
pattern: "*.bai"
authors:
- "@jfy133"