name: "somalier_relate"
description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs
keywords:
  - relatedness
  - QC
  - bam
  - cram
  - vcf
  - gvcf
  - ancestry
  - identity
  - kinship
  - informative sites
  - family
tools:
  - "somalier":
      description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs"
      homepage: "https://github.com/brentp/somalier"
      documentation: "https://github.com/brentp/somalier/blob/master/README.md"
      tool_dev_url: "https://github.com/brentp/somalier"
      doi: "https://doi.org/10.1186/s13073-020-00761-2"
      licence: "MIT License"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - extract:
      type: file
      description: extract file from Somlaier extract
      pattern: "*.somalier"
  - sample_groups:
      type: file
      description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line
      pattern: "*.{txt,csv}"
  - ped:
      type: file
      description: optional path to a ped or fam file indicating the expected relationships among samples
      pattern: "*.{ped,fam}"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - html:
      type: file
      description: html file
      pattern: "*.html"
  - pairs_tsv:
      type: file
      description: tsv file with output stats for pairs of samples
      pattern: "*.pairs.tsv"
  - samples_tsv:
      type: file
      description: tsv file with sample-level information
      pattern: "*.samples.tsv"

authors:
  - "@ashotmarg"