modules/arriba

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

fusionarribadetectionRNA-Seq

https://github.com/nf-core/modules/[...]/modules/nf-core/arriba

Description

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

Input

Name (Type)

Description

Pattern

`meta` (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

`bam` (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

`meta2` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`fasta` (file)

Assembly FASTA file

*.{fasta}

`meta3` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`gtf` (file)

Annotation GTF file

*.{gtf}

`meta4` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`blacklist` (file)

Blacklist file

*.{tsv}

`meta5` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`known_fusions` (file)

Known fusions file

*.{tsv}

`meta6` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`structural_variants` (file)

Structural variants file

*.{tsv}

`meta7` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`tags` (file)

Tags file

*.{tsv}

`meta8` (map)

Groovy Map containing reference information
e.g. [ id:‘test’ ]

`protein_domains` (file)

Protein domains file

*.{gff3}

Output

Name (Type)

Description

Pattern

`meta` (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

`versions` (file)

File containing software versions

versions.yml

`fusions` (file)

File contains fusions which pass all of Arriba’s filters.

*.{fusions.tsv}

`fusions_fail` (file)

File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.

*.{fusions.discarded.tsv}

Tools

arriba
MIT

Fast and accurate gene fusion detection from RNA-Seq data

github.com/suhrig/arriba arriba.readthedocs.io/en/latest https://github.com/suhrig/arriba 10.1101/gr.257246.119