name: deeptools_plotfingerprint
description: plots cumulative reads coverages by BAM file
keywords:
  - plot
  - fingerprint
  - cumulative coverage
  - bam
tools:
  - deeptools:
      description: A set of user-friendly tools for normalization and visualization of deep-sequencing data
      documentation: https://deeptools.readthedocs.io/en/develop/index.html
      tool_dev_url: https://github.com/deeptools/deepTools
      doi: "10.1093/nar/gku365"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - bam:
      type: file
      description: One or more BAM files
      pattern: "*.{bam}"
  - bais:
      type: file
      description: Corresponding BAM file indexes
      pattern: "*.bam.bai"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - pdf:
      type: file
      description: |
        Output figure containing resulting plot
      pattern: "*.{plotFingerprint.pdf}"
  - matrix:
      type: file
      description: |
        Output file summarizing the read counts per bin
      pattern: "*.{plotFingerprint.raw.txt}"
  - metrics:
      type: file
      description: |
        file containing BAM file quality metrics
      pattern: "*.{qcmetrics.txt}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@emiller88"
  - "@drpatelh"
  - "@joseespinosa"
