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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
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description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
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keywords:
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- STR
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- repeat_expansions
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- annotate
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- vcf
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tools:
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- stranger:
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description: Annotate VCF files with str variants
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homepage: https://github.com/moonso/stranger
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documentation: https://github.com/moonso/stranger
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tool_dev_url: https://github.com/moonso/stranger
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doi: "10.5281/zenodo.4548873"
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: VCF with repeat expansions
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pattern: "*.{vcf.gz,vcf}"
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- variant_catalog:
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type: file
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description: json file with repeat expansion sites to genotype
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pattern: "*.{json}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- vcf:
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type: file
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description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
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pattern: "*.{vcf.gz}"
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authors:
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- "@ljmesi"
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