name: pairtools_dedup
description: Find and remove PCR/optical duplicates
keywords:
  - dedup
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 ]
  - input:
      type: file
      description: pair file

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"
  - pairs:
      type: file
      description: Duplicates removed pairs
      pattern: "*.{pairs.gz}"
  - stat:
      type: file
      description: stats of the pairs
      pattern: "*.{pairs.stat}"

authors:
  - "@jianhong"