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
      licence: ["MIT"]
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}"
  - meta2:
      type: map
      description: |
        Groovy Map containing bed information
        e.g. [ id:'test' ]
  - bed:
      type: file
      description: BED file with intersected intervals
      pattern: "*.{bed}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Reference genome FASTA file
      pattern: "*.{fa,fasta}"
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}"
  - per_base_d4:
      type: file
      description: D4 file with per-base coverage
      pattern: "*.{per-base.d4}"
  - 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}"
  - quantized_bed:
      type: file
      description: BED file with binned coverage
      pattern: "*.{quantized.bed.gz}"
  - quantized_csi:
      type: file
      description: Index file for BED file with binned coverage
      pattern: "*.{quantized.bed.gz.csi}"
  - thresholds_bed:
      type: file
      description: BED file with the number of bases in each region that are covered at or above each threshold
      pattern: "*.{thresholds.bed.gz}"
  - thresholds_csi:
      type: file
      description: Index file for BED file with threshold coverage
      pattern: "*.{thresholds.bed.gz.csi}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
  - "@ramprasadn"
  - "@matthdsm"
