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hammerlab / epidisco

Personalized cancer epitope discovery and peptide vaccine prediction pipeline
Apache License 2.0
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Add topiary to the pipeline #158

Closed armish closed 7 years ago

armish commented 7 years ago

Given the name/purpose of this pipeline ("Personalized cancer epitope discovery and peptide vaccine prediction pipeline"), I think we should run topiary by default in addition to vaxrank and include the list of predicted neoepitopes in the results.

smondet commented 7 years ago

It is there: https://github.com/hammerlab/epidisco/blob/0e768f4521853dd635a1783fb1b29fcd1a2ed339/src/lib/parameters.ml#L9 But there is no option to set it to true when using command-line submission

ihodes commented 7 years ago

+ no use of that parameter, either.

smondet commented 7 years ago

@ihodes indeed: https://github.com/hammerlab/epidisco/search?utf8=%E2%9C%93&q=topiary Its use must have been partially removed at some point (I remember adding and running it at some point).

smondet commented 7 years ago

This is relevant: https://github.com/hammerlab/epidisco/commit/150579b2ccbe4247b50b7f074cb646ca7c266eca Does topiary take multiple VCFs now?