name: deeptools_bamcoverage
description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
keywords:
  - sort
tools:
  - deeptools:
      description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
      homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
      documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
      tool_dev_url: https://github.com/deeptools/deepTools/
      doi: "https://doi.org/10.1093/nar/gkw257"
      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}"
  - input_index:
      type: file
      description: BAM/CRAM index file
      pattern: "*.{bai,crai}"
  - fasta:
      type: file
      description: Reference file the CRAM file was created with (required with CRAM input)
      pattern: "*.{fasta,fa}"
  - fasta_fai:
      type: file
      description: Index of the reference file (optional, but recommended)
      pattern: "*.{fai}"

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"
  - bigWig:
      type: file
      description: BigWig file
      pattern: "*.bigWig"
  - bedgraph:
      type: file
      description: Bedgraph file
      pattern: "*.bedgraph"

authors:
  - "@FriederikeHanssen"
  - "@SusiJo"
