This repository provides a selection of example workflows for various tools as a guide for how to compose a submission to the SMC RNA Challenge.
To run test workflow, please run:
./tophat/test/runExample.sh
To run tophat fusion workflow, please make sure you have downloaded the bowtie indexes and two fastq files. Please make sure to edit workflow/smc-tophat-input.json prior to running
cwl-runner workflow/smc-fusion-workflow.cwl workflow/smc-tophat-input.json