Add Arriba (and respective pVACfuse step) to the immuno workflow

wustl-oncology / analysis-wdls

Scalable genomic analysis pipelines, written in WDL

MIT License

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Add Arriba (and respective pVACfuse step) to the immuno workflow #115

Open susannasiebert opened 1 year ago

susannasiebert commented 1 year ago

This is a rebased version of https://github.com/susannasiebert/analysis-wdls/pull/1

susannasiebert commented 1 year ago

@tmooney This was actually something I was wanting to bring up with @malachig and @chrisamiller. Currently pVACfuse ignores a provided star_fusion_file input when it is run with Arriba data because Arriba provides its own Read Support metrics. However, we could potentially still pull Expression metrics from the star_fusion_file. If we allow a star_fusion_file with Arriba, we need to decide which Read Support data takes precedence.

susannasiebert commented 1 year ago

@tmooney I discussed this with Malachi off-thread and I made a new docker image with added support for arriba with a star fusion file. This PR has been updated to take advantage of this update.