mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
a6cb75174b
* Add optional variant catalog input * fix for no variant catalog test Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com> Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
48 lines
1.3 KiB
YAML
48 lines
1.3 KiB
YAML
name: stranger
|
|
description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
|
|
keywords:
|
|
- STR
|
|
- repeat_expansions
|
|
- annotate
|
|
- vcf
|
|
tools:
|
|
- stranger:
|
|
description: Annotate VCF files with str variants
|
|
homepage: https://github.com/moonso/stranger
|
|
documentation: https://github.com/moonso/stranger
|
|
tool_dev_url: https://github.com/moonso/stranger
|
|
doi: "10.5281/zenodo.4548873"
|
|
licence: ["MIT"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- vcf:
|
|
type: file
|
|
description: VCF with repeat expansions
|
|
pattern: "*.{vcf.gz,vcf}"
|
|
- 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', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- vcf:
|
|
type: file
|
|
description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
|
|
pattern: "*.{vcf.gz}"
|
|
|
|
authors:
|
|
- "@ljmesi"
|