name: arriba
description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
keywords:
  - fusion
  - arriba
  - detection
  - RNA-Seq
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}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: Assembly FASTA file
      pattern: "*.{fasta}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - gtf:
      type: file
      description: Annotation GTF file
      pattern: "*.{gtf}"
  - meta4:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - blacklist:
      type: file
      description: Blacklist file
      pattern: "*.{tsv}"
  - meta5:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - known_fusions:
      type: file
      description: Known fusions file
      pattern: "*.{tsv}"
  - meta6:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - structural_variants:
      type: file
      description: Structural variants file
      pattern: "*.{tsv}"
  - meta7:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - tags:
      type: file
      description: Tags file
      pattern: "*.{tsv}"
  - meta8:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'test' ]
  - protein_domains:
      type: file
      description: Protein domains file
      pattern: "*.{gff3}"

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"
  - fusions:
      type: file
      description: File contains fusions which pass all of Arriba's filters.
      pattern: "*.{fusions.tsv}"
  - fusions_fail:
      type: file
      description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.
      pattern: "*.{fusions.discarded.tsv}"

authors:
  - "@praveenraj2018,@rannick"
