name: arriba description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. keywords: - fusion - 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}" - fasta: type: file description: Assembly FASTA file pattern: "*.{fasta}" - 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 ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - 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"