name: arriba_visualisation
description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
keywords:
  - visualisation
  - arriba
tools:
  - arriba:
      description: Fast and accurate gene fusion detection from RNA-Seq data
      homepage: https://github.com/suhrig/arriba
      documentation: https://arriba.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/suhrig/arriba
      doi: "10.1101/gr.257246.119"
      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}"
  - bai:
      type: file
      description: BAMindex file
      pattern: "*.{bai}"
  - fusions:
      type: file
      description: Arriba fusions file
      pattern: "*.{tsv}"
  - gtf:
      type: file
      description: Annotation GTF file
      pattern: "*.{gtf}"

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"
  - pdf:
      type: file
      description: File contains fusions visualisation
      pattern: "*.{pdf}"

authors:
  - "@rannick"
