name: genrich
description: Peak-calling for ChIP-seq and ATAC-seq enrichment experiments
keywords:
  - peak-calling
  - ChIP-seq
  - ATAC-seq
tools:
  - genrich:
      description: |
        Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq).
        It analyzes alignment files generated following the assay and produces a file
        detailing peaks of significant enrichment.
      homepage: https://github.com/jsh58/Genrich
      documentation: https://github.com/jsh58/Genrich#readme
      tool_dev_url: https://github.com/jsh58/Genrich
      doi: ""
      licence: ['MIT']
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - treatment_bam:
      type: file
      description: Coordinate sorted BAM/SAM file from treatment sample
      pattern: "*.{bam,sam}"
  - control_bam:
      type: file
      description: Coordinate sorted BAM/SAM file from control sample
      pattern: "*.{bam,sam}"
  - blacklist_bed:
      type: file
      description: Bed file containing genomic intervals to exclude from the analysis
      pattern: "*.{bed}"
  - save_pvalues:
      type: boolean
      description: Create bedgraph-ish file for p/q-values file
  - save_pileup:
      type: boolean
      description: Create bedgraph-ish file for pileups and p-values
  - save_bed:
      type: boolean
      description: Create BED file for reads/fragments/intervals
  - save_duplicates:
      type: boolean
      description: Create PCR duplicates file (only works if -r option is set)
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - peaks:
      type: file
      description: Output file is in ENCODE narrowPeak format
      pattern: "*.{narrowPeak}"
  - bedgraph_pvalues:
      type: file
      description: bedGraph file containing p/q values
      pattern: "*.{pvalues.bedGraph}"
  - bedgraph_pileup:
      type: file
      description: bedGraph file containing pileups and p-values
      pattern: "*.{pileup.bedGraph}"
  - bed_intervals:
      type: file
      description: Bed file containing annotated intervals
      pattern: "*.{intervals.bed}"
  - duplicates:
      type: file
      description: Text output file containing intervals corresponding to PCR duplicates
      pattern: "*.{intervals.txt}"
  - version:
      type: file
      description: File containing software version
      pattern: "*.{version.txt}"
authors:
  - "@JoseEspinosa"