mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
71 lines
2 KiB
YAML
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 ]
|
|
- input:
|
|
type: file
|
|
description: Sorted and indexed BAM/CRAM/SAM file
|
|
pattern: "*.bam"
|
|
- index:
|
|
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/CRAM/SAM file with local realignment around variants
|
|
pattern: "*.bam"
|
|
- bai:
|
|
type: file
|
|
description: Output BAM Index file
|
|
pattern: "*.bai"
|
|
|
|
authors:
|
|
- "@jfy133"
|