name: lofreq_indelqual
description: Inserts indel qualities in a BAM file
keywords:
  - bam
  - indel
  - qualities
tools:
  - lofreq:
      description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file
      homepage: 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', single_end:false ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.{bam}"
  - fasta:
      type: file
      description: Reference genome FASTA file
      pattern: "*.{fasta}"
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"
  - bam:
      type: file
      description: BAM file with indel qualities inserted into it
      pattern: "*.{bam}"

authors:
  - "@kaurravneet4123"