name: lofreq_callparallel
description: It predicts variants using multiple processors
keywords:
  - variant calling
  - low frequency variant calling
  - 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"]
      identifier: biotools:lofreq
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test' ]
    - bam:
        type: file
        description: Tumor sample sorted BAM file
        pattern: "*.{bam}"
    - bai:
        type: file
        description: BAM index file
        pattern: "*.{bam.bai}"
    - intervals:
        type: file
        description: BED file containing target regions for variant calling
        pattern: "*.{bed}"
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information about the reference fasta
          e.g. [ id:'reference' ]
    - fasta:
        type: file
        description: Reference genome FASTA file
        pattern: "*.{fasta}"
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information about the reference fasta fai
          e.g. [ id:'reference' ]
    - fai:
        type: file
        description: Reference genome FASTA index file
        pattern: "*.{fai}"
output:
  - vcf:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz":
          type: file
          description: Predicted variants file
          pattern: "*.{vcf}"
  - tbi:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*.vcf.gz.tbi":
          type: file
          description: Index of vcf file
          pattern: "*.{vcf.gz.tbi}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@kaurravneet4123"
  - "@bjohnnyd"
maintainers:
  - "@kaurravneet4123"
  - "@bjohnnyd"
  - "@nevinwu"
  - "@AitorPeseta"
