NB This is work in progress - use at your own risk!

Attempt at setting up a pipeline for fusion detection as an addon to the previously existing NGI-RNAseq pipeline.

Usage:

--reads

Path to input reads NB: Must be enclosed in quotes!

 --reads 'path/to/data/sample_*_{1,2}.fastq'

--star-fusion

If this flag is set to true then the pipeline will run STAR-Fusion. True by default

--fusioncatcher

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'

--fc_extra_options

Invoking this flag allows for extra options to be sent directly to Fusion Catcher.

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