name: "somalier_extract"
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 ]
  - input:
      type: file
      description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file
  - input_index:
      type: file
      description: index file of the input data, e.g., bam.bai, cram.crai
  - fasta:
      type: file
      description: The reference fasta file
      pattern: "*.{fasta,fna,fas,fa}"
  - fai:
      type: file
      description: FASTA index file
      pattern: "*.fai"
  - sites:
      type: file
      description: sites file in VCF format which can be taken from https://github.com/brentp/somalier
      pattern: "*.vcf.gz"

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"
  - somalierExtract:
      type: file
      description: binary output file based on extracted sites
      pattern: "*.{somalier}"

authors:
  - "@ashotmarg"