Nextflow Modules
Showing module(s) with keyword "openms"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/openms/decoydatabase | Process | decoy database openms proteomics fasta | Create a decoy peptide database from a standard FASTA database. |
| nf-core/openms/featurefinderidentification | Process | quantification feature detection featureXML openms proteomics | Detects and quantifies features in MS1 data based on peptide identifications (targeted feature extraction). |
| nf-core/openms/fileconverter | Process | file conversion mass spectrometry mzml mzxml openms proteomics | Converts between different mass spectrometry file formats (e.g. mzML, mzXML, mgf, mzData, dta, dta2d, featureXML, consensusXML, idXML). |
| nf-core/openms/filefilter | Process | filter mzML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idconflictresolver | Process | quantification consensusXML openms proteomics | Resolves ambiguous annotations of features with peptide identifications, keeping the best-scoring hit per feature. |
| nf-core/openms/idfilter | Process | filter idXML openms proteomics | Filters peptide/protein identification results by different criteria. |
| nf-core/openms/idmassaccuracy | Process | mass_error openms proteomics | Calculates a distribution of the mass error from given mass spectra and IDs. |
| nf-core/openms/idmerger | Process | merge idXML openms proteomics | Merges several idXML files into one idXML file. |
| nf-core/openms/idripper | Process | split idXML openms proteomics | Split a merged identification file into their originating identification files |
| nf-core/openms/idscoreswitcher | Process | switch score idXML openms proteomics | Switches between different scores of peptide or protein hits in identification data |
| nf-core/openms/mapaligneridentification | Process | alignment retention time trafoXML openms proteomics | Corrects retention time distortions between maps based on common peptide identifications and emits one retention-time transformation (trafoXML) per input map. |
| nf-core/openms/maprttransformer | Process | alignment retention time trafoXML openms proteomics | Applies a retention time transformation (trafoXML) to a spectra or identification/feature map. |
| nf-core/openms/mztabexporter | Process | mztab export openms proteomics | Exports identification and/or quantification results (idXML, featureXML, consensusXML) to the mzTab standard format. |
| nf-core/openms/peakpickerhires | Process | peak picking mzml openms proteomics | A tool for peak detection in high-resolution profile data (Orbitrap or FTICR) |
| nf-core/openms/peptideindexer | Process | refresh idXML openms proteomics | Refreshes the protein references for all peptide hits. |
| nf-core/openms/psmfeatureextractor | Process | features idXML openms percolator proteomics psm | Computes extra features for each input PSM for use with Percolator rescoring. |
| nf-core/openms/textexporter | Process | export openms proteomics text tsv | Exports various OpenMS XML formats (featureXML, consensusXML, idXML, mzML) to a human-readable text format. |
| nf-core/openmsthirdparty/cometadapter | Process | search engine fasta mzml |