nf-core_modules/modules/expansionhunter/meta.yml

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name: expansionhunter
description: Estimate repeat sizes using NGS data
keywords:
- STR
- repeat_expansions
tools:
- expansionhunter:
description: A tool for estimating repeat sizes
homepage: https://github.com/Illumina/ExpansionHunter
documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md
tool_dev_url: None
doi: "10.1093/bioinformatics/btz431"
licence: ["Apache-2.0"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file
pattern: "*.{bam,cram}"
- fasta:
type: file
description: Reference genome
pattern: "*.{fa,fasta}"
- variant_catalog:
type: file
description: json file with repeat expansion sites to genotype
pattern: "*.{json}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', gender:'female' ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf:
type: file
description: VCF with repeat expansions
pattern: "*.{vcf}"
authors:
- "@jemten"