name: pairtools_restrict
description: Assign restriction fragments to pairs
keywords:
  - sort
tools:
  - pairtools:
      description: CLI tools to process mapped Hi-C data
      homepage: http://pairtools.readthedocs.io/
      documentation: http://pairtools.readthedocs.io/
      tool_dev_url: https://github.com/mirnylab/pairtools
      doi: ""
      licence: ["MIT"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - pairs:
      type: file
      description: pairs file
  - frag:
      type: file
      description: |
        a tab-separated BED file with the positions of restriction fragments
        (chrom, start, end).
        Can be generated using cooler digest.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - restrict:
      type: file
      description: Filtered pairs file
      pattern: "*.{pairs.gz}"

authors:
  - "@jianhong"