name: lofreq_callparallel
description: It predicts variants using multiple processors
keywords:
  - call
  - variants
tools:
  - lofreq:
      description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors
      homepage: https://csb5.github.io/lofreq/
      documentation: https://csb5.github.io/lofreq/
      doi: "10.1093/nar/gks918"
      licence: ['MIT']

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: Sorted BAM file
      pattern: "*.{bam}"
  - bai:
      type: file
      description: BAM index file
      pattern: "*.{bai}"
  - fasta:
      type: file
      description: Reference genome FASTA file
      pattern: "*.{fasta}"
  - fai:
      type: file
      description: Reference genome FASTA index file
      pattern: "*.{fai}"

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: Predicted variants file
      pattern: "*.{vcf}"

authors:
  - "@kaurravneet4123"
  - "@bjohnnyd"