name: macs2_callpeak
description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
keywords:
  - alignment
  - atac-seq
  - chip-seq
  - peak-calling
tools:
  - macs2:
      description: Model Based Analysis for ChIP-Seq data
      homepage: None
      documentation: https://docs.csc.fi/apps/macs2/
      tool_dev_url: https://github.com/macs3-project/MACS
      doi: "https://doi.org/10.1101/496521"
      licence: ["BSD"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - ipbam:
      type: file
      description: The ChIP-seq treatment file
  - controlbam:
      type: file
      description: The control file
  - macs2_gsize:
      type: string
      description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
        'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)

output:
  - versions:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - peak:
      type: file
      description: BED file containing annotated peaks
      pattern: "*.gappedPeak,*.narrowPeak}"
  - xls:
      type: file
      description: xls file containing annotated peaks
      pattern: "*.xls"
  - gapped:
      type: file
      description: Optional BED file containing gapped peak
      pattern: "*.gappedPeak"
  - bed:
      type: file
      description: Optional BED file containing peak summits locations for every peak
      pattern: "*.bed"
  - bdg:
      type: file
      description: Optional bedGraph files for input and treatment input samples
      pattern: "*.bdg"

authors:
  - "@ntoda03"
  - "@JoseEspinosa"
  - "@jianhong"