parameters.md

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.

1. Input/Output Options

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.
--debug_level	integer	3	DIA-NN debug/verbosity level (0-4). Higher values produce more verbose logs.
--speclib	string	null	Path to an external spectral library. If provided, the in-silico library generation step is skipped.
--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.
--dda	boolean	false	Explicitly enable DDA mode. Normally auto-detected from the SDRF comment[proteomics data acquisition method] column. Use this flag only when the SDRF lacks the acquisition method. Requires DIA-NN >= 2.3.2.
--light_models	boolean	false	Enable --light-models for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.
--export_quant	boolean	false	Enable --export-quant for fragment-level parquet data export. Requires DIA-NN >= 2.0.
--site_ms1_quant	boolean	false	Enable --site-ms1-quant to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.
--aa_eq	boolean	false	Treat I&L, Q&E, N&D as equivalent amino acids during reannotation. Essential for entrapment FDR benchmarks. Maps to --aa-eq.

DIA-NN 2.5.0 flags (via --extra_args)

The following DIA-NN 2.5.0 flags are not exposed as pipeline parameters but can be passed via --extra_args. See Fine-Tuning Deep Learning Models for the complete workflow.

DIA-NN flag	Description
--tokens <file>	Tokenizer dictionary mapping modified residues to neural network token IDs (0-255).
--rt-model <file>	Fine-tuned retention time prediction model (.pt PyTorch file).
--fr-model <file>	Fine-tuned fragment ion prediction model (.pt file). Quality-sensitive — verify vs base model.
--im-model <file>	Fine-tuned ion mobility prediction model (.pt file).
--tune-lib <file>	Spectral library for fine-tuning (.parquet). Requires --tune-rt and/or --tune-im.
--tune-rt	Fine-tune the RT deep learning predictor. Requires --tune-lib.
--tune-im	Fine-tune the IM deep learning predictor. Requires --tune-lib.
--tune-fr	Fine-tune the fragmentation predictor. Requires --tune-lib. Use with caution.
--tune-lr <X>	Fine-tuning learning rate (default: 0.0005).
--tune-restrict-layers	Keep RNN layer weights fixed during fine-tuning (except cysteine embeddings).
--tune-level <N>	Limit fine-tuning to a specific model distillation level (0, 1, or 2).

Note: --parent and --aa-eq are blocked from --extra_args — they are managed as pipeline parameters (--aa_eq). --parent is container-managed and overriding it would break model discovery.

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
--tims_sum	boolean	false	Enable --quant-tims-sum for slice/scanning timsTOF methods (highly recommended for Synchro-PASEF).
--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.
--empirical_assembly_log	string	null	Path to a pre-existing empirical assembly log file. Only used when --skip_preliminary_analysis true and --speclib are set.
--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.
--normalize	boolean	true	Enable cross-run normalisation in DIA-NN. Set to false to add --no-norm.
--report_decoys	boolean	false	Include decoy PSMs in the main .parquet report (DIA-NN 2.0+ only).
--export_xic	boolean	false	Extract MS1/fragment chromatograms for identified precursors (equivalent to the XICs option in the DIA-NN GUI).
--scoring_mode	string	generic	DIA-NN scoring mode: generic (default, maximizes IDs), proteoforms (recommended for proteogenomics/variant detection, requires >= 2.0), peptidoforms (extra q-values for PTM analysis).
--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. DDA Mode

Parameter	Type	Default	Description
--dda	boolean	false	Explicitly enable DDA mode when SDRF lacks the acquisition method column. Normally DDA is auto-detected from the SDRF comment[proteomics data acquisition method]. Requires DIA-NN >= 2.3.2 (use -profile diann_v2_3_2). Beta feature.

Note: DDA mode is auto-detected from the SDRF when the comment[proteomics data acquisition method] column contains data-dependent acquisition. The --dda flag is only needed as a fallback when the SDRF does not include this column. DDA requires DIA-NN >= 2.3.2 (-profile diann_v2_3_2).

13. InfinDIA (Experimental)

Parameter	Type	Default	Description
--enable_infin_dia	boolean	false	Enable InfinDIA for ultra-large search spaces. Requires DIA-NN >= 2.3.0. Experimental.
--pre_select	integer	null	Precursor limit (--pre-select N) for InfinDIA pre-search.

Note: InfinDIA requires DIA-NN >= 2.3.0 and is considered experimental.

14. 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.
--precursor_qvalue	number	0.01	Precursor-level q-value threshold for the DIA-NN main report. Maps to --qvalue.
--matrix_qvalue	number	0.01	Q-value threshold for DIA-NN output matrices (pr_matrix, pg_matrix). Maps to --matrix-qvalue.
--matrix_spec_q	number	0.05	Run-specific protein q-value for protein/gene matrices. Maps to --matrix-spec-q.

15. 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.