FragPipe and DIA-NN Terra workflows from raw proteomics processing - Githubissues

broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

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FragPipe and DIA-NN Terra workflows from raw proteomics processing #38

Closed Munchic closed 1 year ago

Munchic commented 1 year ago

FragPipe

Terra workflows FragPipe 19.0 CLI
Support for all Thermo and Bruker raw DDA file formats
Support for easyPQP spectral library creation from DDA runs
Automated default manifest creation (can take custom manifests)
Direct configuration from GUI via .workflow configuration files
Workflow parameters documentation

DIA-NN

Terra workflow for DIA-NN 1.8.1 CLI
Support for all Thermo and Bruker raw DIA file formats
Spectral library generation and combining
Scatter-gather parallelized implementation for first pass searches
Workflow parameters documentation