Allow clinical types in immuno workflow

genome / analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

MIT License

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Allow clinical types in immuno workflow #670

Closed johnegarza closed 4 years ago

johnegarza commented 5 years ago

https://github.com/genome/analysis-workflows/blob/a3e26136043c03192c38c335316d2d36e3e67478/definitions/pipelines/immuno.cwl#L731

The immuno workflow should be modified to allow the user to optionally specify clinical HLA types. These should be intersected with the optitype output using a filtering script, then passed to pvacseq

chrisamiller commented 4 years ago

This exists in the currently implemented immuno workflow, as far as i can tell. @johnegarza, please reopen if I'm mistaken