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TalusBio / nf-encyclopedia

A NextFlow pipeline for chromatogram library DIA proteomics workflows
Apache License 2.0
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Filter MSstats for accepted proteins, add tests, and improve code #26

Closed wfondrie closed 2 years ago

wfondrie commented 2 years ago

This PR add the option to use Walnut when no DLIB/ELIB is provided. Additionally, it removes the aggregate options, which for now may be problematic.

wfondrie commented 2 years ago

Alas, I think I'm not going to merge the Walnut changes.

Running the Prosit DLIB this way yielded almost an identical number of peptides as before - I think the DLIB/ELIB file is only used during the "global" step to get the peptide <-> protein mapping.