name: mosdepth
description: Calculates genome-wide sequencing coverage.
keywords:
  - mosdepth
  - bam
  - cram
  - coverage
tools:
  - mosdepth:
      description: |
        Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
      documentation: https://github.com/brentp/mosdepth
      doi: 10.1093/bioinformatics/btx699
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Input BAM/CRAM file
      pattern: "*.{bam,cram}"
  - bai:
      type: file
      description: Index for BAM/CRAM file
      pattern: "*.{bai,crai}"
  - bed:
      type: file
      description: BED file with intersected intervals
      pattern: "*.{bed}"
  - window_size:
      type: integer
      description: Window size
      pattern: "[0-9]+"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - global_txt:
      type: file
      description: Text file with global cumulative coverage distribution
      pattern: "*.{global.dist.txt}"
  - regions_txt:
      type: file
      description: Text file with region cumulative coverage distribution
      pattern: "*.{region.dist.txt}"
  - summary_txt:
      type: file
      description: Text file with summary mean depths per chromosome and regions
      pattern: "*.{summary.txt}"
  - per_base_bed:
      type: file
      description: BED file with per-base coverage
      pattern: "*.{per-base.bed.gz}"
  - per_base_csi:
      type: file
      description: Index file for BED file with per-base coverage
      pattern: "*.{per-base.bed.gz.csi}"
  - regions_bed:
      type: file
      description: BED file with per-region coverage
      pattern: "*.{regions.bed.gz}"
  - regions_csi:
      type: file
      description: Index file for BED file with per-region coverage
      pattern: "*.{regions.bed.gz.csi}"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
authors:
    - "@joseespinosa"
    - "@drpatelh"