name: seacr_callpeak
description: Call peaks using SEACR on sequenced reads in bedgraph format
keywords:
  - peak-caller
  - peaks
  - bedgraph
  - cut&tag
  - cut&run
  - chromatin
  - seacr
tools:
  - seacr:
    description: |
      SEACR is intended to call peaks and enriched regions from sparse CUT&RUN
      or chromatin profiling data in which background is dominated by "zeroes"
      (i.e. regions with no read coverage).
    homepage: https://github.com/FredHutch/SEACR
    documentation: https://github.com/FredHutch/SEACR
    licence: ["GPL-2.0-only"]
input:
  - meta:
    type: map
    description: |
      Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bedgraph:
    type: file
    description: |
      The target bedgraph file from which the peaks will be calculated.
  - ctrlbedgraph:
    type: file
    description: |
      Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
  - threshold:
    type: value
    description: |
      Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
output:
  - meta:
    type: map
    description: |
      Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
    type: file
    description: Bed file containing the calculated peaks.
    pattern: "*.bed"
  - versions:
    type: file
    description: File containing software versions
    pattern: "versions.yml"
authors:
  - "@chris-cheshire"