Initial release of nf-core/proteomicslfq, created with the nf-core template.

Added

The initial version of the pipeline features the following steps:

• (optional) Conversion of spectra data to indexedMzML: Using ThermoRawFileParser if Thermo Raw or using OpenMS’ FileConverter if just an index is missing
• (optional) Decoy database generation for the provided DB (fasta) with OpenMS
• Database search with either MSGF+ and/or Comet through OpenMS adapters
• Re-mapping potentially identified peptides to the input database for consistency and error-checking (using OpenMS’ PeptideIndexer)
• PSM rescoring using PSMFeatureExtractor and Percolator or a PeptideProphet-like distribution fitting approach in OpenMS
• If multiple search engines were chosen, the results are combined with OpenMS’ ConsensusID
• If multiple search engines were chosen, a combined FDR is calculated
• Single run PSM/Peptide-level FDR filtering
• If localization of modifications was requested, Luciphor2 is applied via the OpenMS adapter
• Protein inference and labelfree quantification based on spectral counting or MS1 feature detection, alignment and integration with OpenMS’ ProteomicsLFQ. Performs an additional experiment-wide FDR filter on protein level (and if requested peptide/PSM level).

Known issues

If you experience nextflow running forever after a failed step, try settings errorStrategy = terminate. See the corresponding nextflow issue.

Fixed

Dependencies

Deprecated