name: strelka_somatic
description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
keywords:
  - variant calling
  - 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', single_end:false ]
  - cram_normal:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - crai_normal:
      type: file
      description: BAM/CRAM/SAM index file
      pattern: "*.{bai,crai,sai}"
  - cram_tumor:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - crai_tumor:
      type: file
      description: BAM/CRAM/SAM index file
      pattern: "*.{bai,crai,sai}"
  - manta_candidate_small_indels:
      type: file
      description: VCF.gz file
      pattern: "*.{vcf.gz}"
  - manta_candidate_small_indels_tbi:
      type: file
      description: VCF.gz index file
      pattern: "*.tbi"
  - 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_tbi:
      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', single_end:false ]
  - vcf_indels:
      type: file
      description: Gzipped VCF file containing variants
      pattern: "*.{vcf.gz}"
  - vcf_indels_tbi:
      type: file
      description: Index for gzipped VCF file containing variants
      pattern: "*.{vcf.gz.tbi}"
  - vcf_snvs:
      type: file
      description: Gzipped VCF file containing variants
      pattern: "*.{vcf.gz}"
  - vcf_snvs_tbi:
      type: file
      description: Index for gzipped VCF file containing variants
      pattern: "*.{vcf.gz.tbi}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@drpatelh"