name: fusionreport
description: fusionreport
keywords:
  - sort
tools:
  - fusionreport:
      description: fusionreport
      homepage: https://github.com/matq007/fusion-report
      documentation: https://matq007.github.io/fusion-report/#/
      doi: "10.1101/011650"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reference:
      type: path
      description: Path to fusionreport references
      pattern: "*"
  - arriba_fusions:
      type: path
      description: File
      pattern: "*.fusions.tsv"
  - pizzly_fusions:
      type: path
      description: File containing fusions from pizzly
      pattern: "*.pizzly.txt"
  - squid_fusions:
      type: path
      description: File containing fusions from squid
      pattern: "*.annotated.txt"
  - starfusion_fusions:
      type: path
      description: File containing fusions from STARfusion
      pattern: "*.starfusion.fusion_predictions.tsv"
  - fusioncatcher_fusions:
      type: path
      description: File containing fusions from fusioncatcher
      pattern: "*.fusions.tsv"

output:
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fusion_list:
      type: file
      description: File containing the summary of all fusions fed-in
      pattern: "*.tsv"
  - report:
      type: file
      description: HTML files
      pattern: "*.html"

authors:
  - "@praveenraj2018, @rannick"
