Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
meta2{:bash}
Groovy Map containing reference information e.g. [ id:‘test’ ]
fasta{:bash}
Assembly FASTA file
*.{fasta}
meta3{:bash}
gtf{:bash}
Annotation GTF file
*.{gtf}
blacklist{:bash}
Blacklist file
*.{tsv}
known_fusions{:bash}
Known fusions file
cytobands{:bash}
Cytobands file
protein_domains{:bash}
Protein domains file
*.{gff3}
fusions{:bash}
*.fusions.tsv{:bash}
File contains fusions which pass all of Arriba’s filters.
*.{fusions.tsv}
fusions_fail{:bash}
*.fusions.discarded.tsv{:bash}
File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.
*.{fusions.discarded.tsv}
versions_arriba{:bash}
${task.process}{:bash}
:string
The name of the process
arriba{:bash}
The name of the tool
arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Fast and accurate gene fusion detection from RNA-Seq data
