name: lofreq_call
description: Lofreq subcommand to call low frequency variants from alignments
keywords:
  - variant calling
  - low frequency variant calling
  - lofreq
  - lofreq/call
tools:
  - lofreq:
      description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
      homepage: https://csb5.github.io/lofreq/
      documentation: https://csb5.github.io/lofreq/commands/
      doi: "10.1093/nar/gks918 "
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM input file
      pattern: "*.{bam}"
  - fasta:
      type: file
      description: The reference fasta file

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
  - vcf:
      type: file
      description: VCF output file
      pattern: "*.{vcf}"

authors:
  - "@bjohnnyd"