name: strelka_germline
description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation
keywords:
  - variantcalling
  - germline
  - wgs
  - vcf
  - variants
tools:
  - strelka:
      description: Strelka calls somatic and germline small variants from mapped sequencing reads
      homepage: https://github.com/Illumina/strelka
      documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
      tool_dev_url: https://github.com/Illumina/strelka
      doi: 10.1038/s41592-018-0051-x
      licence: ["GPL v3"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - input:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - input_index:
      type: file
      description: BAM/CRAI index file
      pattern: "*.{bai,crai}"
  - fasta:
      type: file
      description: Genome reference FASTA file
      pattern: "*.{fa,fasta}"
  - fai:
      type: file
      description: Genome reference FASTA index file
      pattern: "*.{fa.fai,fasta.fai}"
  - target_bed:
      type: file
      description: BED file containing target regions for variant calling
      pattern: "*.{bed}"
  - target_bed_index:
      type: file
      description: Index for BED file containing target regions for variant calling
      pattern: "*.{bed.tbi}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test']
  - vcf:
      type: file
      description: gzipped germline variant file
      pattern: "*.{vcf.gz}"
  - vcf_tbi:
      type: file
      description: index file for the vcf file
      pattern: "*.vcf.gz.tbi"
  - genome_vcf:
      type: file
      description: variant records and compressed non-variant blocks
      pattern: "*_genome.vcf.gz"
  - genome_vcf_tbi:
      type: file
      description: index file for the genome_vcf file
      pattern: "*_genome.vcf.gz.tbi"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@arontommi"
maintainers:
  - "@arontommi"
