This pipeline has been moved to the new nf-core project. You can now find it here:
If you have any problems with the pipeline, please create an issue at the above repository instead.
To find out more about nf-core, visit http://nf-co.re/
This repository will be archived to maintain the released versions for future reruns, in the spirit of full reproducibility.
If you have any questions, please get in touch: support@ngisweden.se
// Phil Ewels, 2018-10-05
Attempt at setting up a pipeline for fusion detection as an addon to the previously existing NGI-RNAseq pipeline.
Path to input reads NB: Must be enclosed in quotes!
--reads 'path/to/data/sample_*_{1,2}.fastq'
If this flag is set to true then the pipeline will run STAR-Fusion. True by default
If this flag is set to true then the pipeline will run Fusion Catcher. True by default
More than one of these can be true at a time.
Example usage if you wish to run both STAR-fusion and Fusion Catcher
nextflow run /NGI-RNAfusion/main.nf --star --fusioncatcher --reads 'SRR5665649_{1,2}*.gz'
Invoking this flag allows for extra options to be sent directly to Fusion Catcher.
