name: pairtools_parse
description: Find ligation junctions in .sam, make .pairs
keywords:
  - parse
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 ]
  - bam:
      type: file
      description: BAM/CRAM/SAM file
      pattern: "*.{bam,cram,sam}"
  - chromsizes:
      type: file
      description: chromosome size 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"
  - pairsam:
      type: file
      description: parsed pair file
      pattern: "*.{pairsam.gz}"
  - stat:
      type: file
      description: stats of the pairs
      pattern: "*.{pairsam.stat}"

authors:
  - "@jianhong"