name: samtools_depth
description: Computes the depth at each position or region.
keywords:
  - depth
  - samtools
  - statistics
  - coverage
tools:
  - samtools:
      description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
      homepage: http://www.htslib.org
      documentation: http://www.htslib.org/doc/samtools-depth.html
      tool_dev_url: https://github.com/samtools/samtools
      doi: "10.1093/bioinformatics/btp352"
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: sorted BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"

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"
  - tsv:
      type: file
      description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position
      pattern: "*.{tsv}"

authors:
  - "@louperelo"