references.md

nfcore/rnafusion: Download references for tools

Downloading references manually is a tedious long process. To make the pipeline easier to work with, we provide a script to download all necessary references for fusion detection tools.

TL;DR: Make sure to download the correct references for your need!

nextflow run nf-core/rnafusion/download-references.nf --help

Download all references

# Replace <COSMIC_USER> and <COSMIC_PASSWD> with yout credentials from COSMIC
nextflow run nf-core/rnafusion/download-references.nf \
  --download_all \
  --outdir <PATH> \
  --cosmic_usr <COSMIC_USER> --cosmic_passwd <COSMIC_PASSWD>

Download specific references

# Example of downloading specific tools
nextflow run nf-core/rnafusion/download-references.nf \
--arriba \
--outdir <PATH>

Tool reference requirements

Tool	FASTA	GTF	STAR-index	Other
Arriba	✅	✅	✅	custom_reference
EricScript	❌	❌	❌	custom_reference
FusionCatcher	❌	❌	❌	custom_reference
Fusion-Inspector	✅	✅	✅	ctat_genome_lib
fusion-report	❌	❌	❌	databases
Pizzly	❌	✅	✅	cDNA
Squid	❌	✅	✅	-
Star-Fusion	✅	✅	✅	ctat_genome_lib