nf-core_modules/modules/arriba/meta.yml
2022-05-09 14:55:59 +02:00

74 lines
2 KiB
YAML

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}"
- blacklist:
type: file
description: Blacklist file
pattern: "*.{tsv}"
- known_fusions:
type: file
description: Known fusions file
pattern: "*.{tsv}"
- structural_variants:
type: file
description: Structural variants file
pattern: "*.{tsv}"
- tags:
type: file
description: Tags file
pattern: "*.{tsv}"
- 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"