name: fusioncatcher
description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
keywords:
  - fusioncatcher
tools:
  - fusioncatcher:
      description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
      homepage: https://github.com/ndaniel/fusioncatcher
      documentation: https://github.com/ndaniel/fusioncatcher/wiki
      tool_dev_url: https://github.com/ndaniel/fusioncatcher
      doi: "10.1101/011650v1"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: FASTQ file
      pattern: "*.{fastq}"
  - reference:
      type: directory
      description: Path to fusioncatcher references
      pattern: "*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fusions:
      type: file
      description: Final list of candidate fusion genes
      pattern: "*.fusioncatcher.fusion-genes.txt"
  - summary:
      type: file
      description: Summary of fusion results
      pattern: "*.fusioncatcher_summary.txt"
  - log:
      type: file
      description: Log of fusion results
      pattern: "*.fusioncatcher.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@praveenraj2018. @rannick"
