name: tiddit_cov
description: Computes the coverage of different regions from the bam file.
keywords:
  - coverage
  - bam
  - statistics
  - chromosomal rearrangements
tools:
  - tiddit:
      description: TIDDIT - structural variant calling.
      homepage: https://github.com/SciLifeLab/TIDDIT
      documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md
      doi: "10.12688/f1000research.11168.1"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: |
        Reference genome file. Only needed when passing in CRAM instead of BAM.
        If not using CRAM, please pass an empty file instead.
      pattern: "*.fasta"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - cov:
      type: file
      description: The coverage of different regions. Optional.
      pattern: "*.tab"
  - wig:
      type: file
      description: The coverage of different regions in WIG format. Optional.
      pattern: "*.wig"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@projectoriented"
  - "@ramprasadn"
