bigbio/quantmsdiann: Parameters
This document lists every pipeline parameter organised by category. Default values come from nextflow.config; types and constraints come from nextflow_schema.json.
| Parameter |
Type |
Default |
Description |
--input |
string (file-path) |
required |
URI/path to an SDRF file with .sdrf, .tsv, or .csv extension. Parameters such as enzyme, fixed modifications, and acquisition method are read from the SDRF. |
--database |
string (file-path) |
required |
Path to a FASTA protein database. Must not contain decoys for DIA data. |
--outdir |
string (directory-path) |
./results |
The output directory where results will be saved. |
--publish_dir_mode |
string |
copy |
Method used to save pipeline results. One of: symlink, rellink, link, copy, copyNoFollow, move. |
--root_folder |
string |
null |
Root folder in which spectrum files specified in the SDRF are searched. Used when you have a local copy of the experiment. |
--local_input_type |
string |
mzML |
Overwrite the file type/extension of filenames in the SDRF when using --root_folder. One of: mzML, raw, d, dia. Compressed variants (.gz, .tar, .tar.gz, .zip) are supported for mzML, raw, and d. |
--email |
string |
null |
Email address for completion summary. |
2. SDRF Validation
| Parameter |
Type |
Default |
Description |
--use_ols_cache_only |
boolean |
true |
Use only the cached Ontology Lookup Service (OLS) for ontology term validation. Set to false to allow network requests. |
3. File Preparation (Spectrum Preprocessing)
| Parameter |
Type |
Default |
Description |
--reindex_mzml |
boolean |
true |
Force re-indexing of input mzML files at the start of the pipeline for safety. |
--mzml_statistics |
boolean |
false |
Compute MS1/MS2 statistics from mzML files. Generates *_ms_info.parquet files for QC. Bruker .d files are always skipped. |
--mzml_features |
boolean |
false |
Compute MS1-level features during the mzML statistics step. Only available for mzML files. |
4. Search Parameters
| Parameter |
Type |
Default |
Description |
--met_excision |
boolean |
true |
Account for N-terminal methionine excision during database search. |
--allowed_missed_cleavages |
integer |
2 |
Maximum number of allowed missed enzyme cleavages per peptide. |
--precursor_mass_tolerance |
integer |
5 |
Precursor mass tolerance for database search (see --precursor_mass_tolerance_unit). Can be overridden; falls back to SDRF value. |
--precursor_mass_tolerance_unit |
string |
ppm |
Precursor mass tolerance unit. One of: ppm, Da. |
--fragment_mass_tolerance |
number |
0.03 |
Fragment mass tolerance for database search (see --fragment_mass_tolerance_unit). |
--fragment_mass_tolerance_unit |
string |
Da |
Fragment mass tolerance unit. One of: ppm, Da. |
--variable_mods |
string |
Oxidation (M) |
Comma-separated variable modifications in Unimod format (e.g. Oxidation (M),Carbamidomethyl (C)). Can be overridden; falls back to SDRF. |
--min_precursor_charge |
integer |
2 |
Minimum precursor ion charge. |
--max_precursor_charge |
integer |
4 |
Maximum precursor ion charge. |
--min_peptide_length |
integer |
6 |
Minimum peptide length to consider. |
--max_peptide_length |
integer |
40 |
Maximum peptide length to consider. |
--max_mods |
integer |
3 |
Maximum number of variable modifications per peptide. |
--min_pr_mz |
number |
400 |
Minimum precursor m/z for in-silico library generation or library-free search. |
--max_pr_mz |
number |
2400 |
Maximum precursor m/z for in-silico library generation or library-free search. |
--min_fr_mz |
number |
100 |
Minimum fragment m/z for in-silico library generation or library-free search. |
--max_fr_mz |
number |
1800 |
Maximum fragment m/z for in-silico library generation or library-free search. |
5. DIA-NN General
| Parameter |
Type |
Default |
Description |
--diann_version |
string |
1.8.1 |
DIA-NN version used by the workflow. Controls version-dependent flags (e.g. --monitor-mod for 1.8.x). See DIA-NN Version Selection. |
--diann_debug |
integer |
3 |
DIA-NN debug/verbosity level (0-4). Higher values produce more verbose logs. |
--diann_speclib |
string |
null |
Path to an external spectral library. If provided, the in-silico library generation step is skipped. |
--diann_extra_args |
string |
null |
Extra arguments appended to all DIA-NN steps. Flags incompatible with a step are automatically stripped with a warning. See Passing Extra Arguments to DIA-NN. |
6. Mass Accuracy & Calibration
| Parameter |
Type |
Default |
Description |
--mass_acc_automatic |
boolean |
true |
Automatically determine MS2 mass accuracy. When true, --mass_acc_ms2 is ignored during preliminary analysis. |
--mass_acc_ms1 |
number |
15 |
MS1 mass accuracy in ppm. Overrides automatic calibration when --mass_acc_automatic false. Maps to DIA-NN --mass-acc-ms1. |
--mass_acc_ms2 |
number |
15 |
MS2 mass accuracy in ppm. Overrides automatic calibration when --mass_acc_automatic false. Maps to DIA-NN --mass-acc. |
--scan_window |
integer |
8 |
Scan window radius. Should approximate the average number of data points per peak. |
--scan_window_automatic |
boolean |
true |
Automatically determine the scan window. When true, --scan_window is ignored. |
--quick_mass_acc |
boolean |
true |
Use a fast heuristic algorithm for mass accuracy calibration instead of ID-number optimisation. |
--performance_mode |
boolean |
true |
Enable low-RAM, high-speed mode. Adds --min-corr 2 --corr-diff 1 --time-corr-only to DIA-NN. |
7. Bruker/timsTOF
| Parameter |
Type |
Default |
Description |
--diann_tims_sum |
boolean |
false |
Enable --quant-tims-sum for slice/scanning timsTOF methods (highly recommended for Synchro-PASEF). |
--diann_im_window |
number |
null |
Set --im-window to ensure the IM extraction window is not smaller than the specified value. |
8. PTM Localization
| Parameter |
Type |
Default |
Description |
--enable_mod_localization |
boolean |
false |
Enable modification localization scoring in DIA-NN via --monitor-mod (DIA-NN 1.8.x only; automatic in 2.0+). |
--mod_localization |
string |
Phospho (S),Phospho (T),Phospho (Y) |
Comma-separated modification names or UniMod accessions for PTM localization (e.g. UniMod:21). |
9. Library Generation
| Parameter |
Type |
Default |
Description |
--save_speclib_tsv |
boolean |
false |
Publish the TSV spectral library from in-silico library generation to library_generation/. |
10. Preliminary Analysis
| Parameter |
Type |
Default |
Description |
--skip_preliminary_analysis |
boolean |
false |
Skip preliminary analysis. Use the provided spectral library as-is instead of generating a local consensus library. |
--random_preanalysis |
boolean |
false |
Enable random selection of spectrum files for empirical library generation. |
--random_preanalysis_seed |
integer |
42 |
Random seed for file selection when --random_preanalysis is enabled. |
--empirical_assembly_ms_n |
integer |
200 |
Number of randomly selected spectrum files when --random_preanalysis is enabled. |
11. Quantification & Output
| Parameter |
Type |
Default |
Description |
--pg_level |
integer |
2 |
Protein inference mode. 0 = isoforms, 1 = protein names (from FASTA), 2 = genes (default). |
--species_genes |
boolean |
false |
Add the organism identifier to gene names in DIA-NN output. |
--diann_normalize |
boolean |
true |
Enable cross-run normalisation in DIA-NN. Set to false to add --no-norm. |
--diann_report_decoys |
boolean |
false |
Include decoy PSMs in the main .parquet report (DIA-NN 2.0+ only). |
--diann_export_xic |
boolean |
false |
Extract MS1/fragment chromatograms for identified precursors (equivalent to the XICs option in the DIA-NN GUI). |
--diann_no_peptidoforms |
boolean |
false |
Disable automatic peptidoform scoring when variable modifications are declared (not recommended by DIA-NN). |
--diann_use_quant |
boolean |
true |
Reuse existing .quant files if available (--use-quant). |
--quantums |
boolean |
false |
Enable QuantUMS quantification (requires DIA-NN >= 1.9.2). When false, the pipeline passes --direct-quant to use legacy quantification (only for DIA-NN >= 1.9.2; silently skipped for 1.8.x where direct quant is the only mode). |
--quantums_train_runs |
string |
null |
Run index range for QuantUMS training (e.g. 0:5). Maps to --quant-train-runs. Requires DIA-NN >= 1.9.2. |
--quantums_sel_runs |
integer |
null |
Number of automatically selected runs for QuantUMS training. Must be >= 6. Maps to --quant-sel-runs. Requires DIA-NN >= 1.9.2. |
--quantums_params |
string |
null |
Pre-calculated QuantUMS parameters. Maps to --quant-params. Requires DIA-NN >= 1.9.2. |
12. Quality Control
| Parameter |
Type |
Default |
Description |
--enable_pmultiqc |
boolean |
true |
Generate the pmultiqc QC report. |
--pmultiqc_idxml_skip |
boolean |
true |
Skip idXML files (do not generate search engine score plots) in the pmultiqc report. |
--contaminant_string |
string |
CONT |
Contaminant affix string for pmultiqc. Maps to --contaminant_affix in pmultiqc. |
--protein_level_fdr_cutoff |
number |
0.01 |
Experiment-wide protein (group)-level FDR cutoff. |
13. MultiQC & Reporting
| Parameter |
Type |
Default |
Description |
--multiqc_config |
string (file-path) |
null |
Custom config file to supply to MultiQC. |
--multiqc_title |
string |
null |
MultiQC report title. Used as page header and filename. |
--multiqc_logo |
string |
null |
Custom logo file for MultiQC. Must also be referenced in the MultiQC config file. |
--skip_table_plots |
boolean |
false |
Skip protein/peptide table plots in pmultiqc for large datasets. |
--max_multiqc_email_size |
string |
25.MB |
File size limit when attaching MultiQC reports to summary emails. |
--multiqc_methods_description |
string |
null |
Custom MultiQC YAML file containing an HTML methods description. |