Nextflow Modules
Showing module(s) with keyword "diann"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/diann/insilicolibrarygeneration | Process | diann spectral library proteomics deep learning dia | Generate in silico predicted spectral library using DIA-NN deep learning predictor. This module uses DIA-NN software for data-independent acquisition (DIA) proteomics data processing. Output materials should include attribution: "Generated using DIA-NN". |
| nf-core/dia_proteomics_analysis | Workflow | diann proteomics dia quantification spectral library quantms-utils | Complete DIA-NN proteomics analysis pipeline including in-silico library generation, preliminary analysis, empirical library assembly, individual analysis, and final quantification. This subworkflow combines DIA-NN modules with quantms-utils for comprehensive data-independent acquisition (DIA) proteomics data processing. |
| nf-core/easypqp/library | Process | proteomics spectral library dia openswath diann | Generate a spectral library (TSV) from EasyPQP PSM and peak pickle files. |
| nf-core/parsesdrf/convert | Process | sdrf sdrf-pipelines samplesheet proteomics immunopeptidomics mhcquant openms maxquant msstats normalyzerde diann metadata | Convert an SDRF (Sample and Data Relationship Format) file into a pipeline-specific samplesheet/configuration using the `parse_sdrf convert-<format>` subcommands of the sdrf-pipelines package. The chosen `format` selects the subcommand; the module owns the output filenames and emits one tuple per supported format (mhcquant, openms, maxquant, msstats, normalyzerde, diann). |
| nf-core/quantmsutils/diann2mztab | Process | quantms-utils diann mztab msstats triqler proteomics | Convert DIA-NN results to mzTab, MSstats, and Triqler formats using quantms-utils |
| nf-core/quantmsutils/dianncfg | Process | quantms-utils diann configuration enzyme modifications | Generate DIA-NN configuration arguments from enzyme and Unimod modification parameters. This module uses quantms-utils to convert enzyme and modification specifications into DIA-NN-compatible command-line arguments. Only supports Unimod modifications. For custom modifications, pass arguments directly to the DIANN module. |