name: starfusion
description: Fast and Accurate Fusion Transcript Detection from RNA-Seq
keywords:
  - Fusion
tools:
  - star-fusion:
      description: Fast and Accurate Fusion Transcript Detection from RNA-Seq
      homepage: https://github.com/STAR-Fusion/STAR-Fusion
      documentation: https://github.com/STAR-Fusion/STAR-Fusion/wiki
      tool_dev_url: https://github.com/STAR-Fusion/STAR-Fusion/releases
      doi: "10.1101/120295v1"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - genome_lib:
      type: path
      description: STAR-fusion reference genome lib folder
  - junction:
      type: file
      description: Chimeric junction output from STAR aligner
      pattern: "*.{out.junction}"
  - reference:
      type: directory
      description: Reference dir
      pattern: "ctat_genome_lib_build_dir"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "*.{versions.yml}"
  - fusions:
      type: file
      description: Fusion events from STAR-fusion
      pattern: "*.{fusion_predictions.tsv}"
  - abridged:
      type: file
      description: Fusion events from STAR-fusion
      pattern: "*.{fusion.abridged.tsv}"
  - coding_effect:
      type: file
      description: Fusion events from STAR-fusion
      pattern: "*.{coding_effect.tsv}"

authors:
  - "@praveenraj2018"
