name: "bbmap_pileup"
description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
keywords:
  - fasta
  - genome
  - coverage
tools:
  - bbmap:
      description: BBMap is a short read aligner, as well as various other bioinformatic tools.
      homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
      tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
      doi: ""
      licence: ["UC-LBL license (see package)"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: 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 ]
  - stats:
      type: file
      description: Per-scaffold coverage info
      pattern: "*.stats.txt"
  - hist:
      type: file
      description: "Histogram of # occurrences of each depth level"
      pattern: "*.hist.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@Emiller88"