How to run immuno.cwl pipeline

[dxkeac]

Hello, I am a CWL rookie. I want to use the Immuno.cwl to detect neoantigens. It makes me confused that (https://github.com/genome/analysis-workflows) contains too many CWL processes. Is there a description of the steps from the FASTQ file to the neoantigens? Thanks.

[susannasiebert]

Hi @dxkeac,

Thanks for your interest in our workflows. This repo contains all of the workflows utilized at our institution so it can be a bit confusing at first. The immuno.cwl you're looking for can be found here. The reason you're seeing so many cwl files in this repo is that a cwl workflow is made up of steps, which in itself can be other workflows or tool cwls. In case of the immuno.cwl it calls various other subworkflows, e.g. for alignment, variant & fusion calling, rnasq, hla typing, etc up to running pVACseq for neoepitope prediction. It's probably our most complex workflow. You might find our wiki documentation for this workflow helpful for starts.

Best,
Susanna