CLI Reference¶

pmultiqc extends the MultiQC command-line interface with proteomics-specific options. All options are passed as arguments to the multiqc command after installing pmultiqc.

Basic Invocation¶

multiqc [ANALYSIS_DIR] -o [OUTPUT_DIR] [OPTIONS]

Each plugin is activated by passing its corresponding flag. Only one plugin should be active per run.

# quantms pipeline output
multiqc --quantms-plugin /path/to/results -o ./report

# MaxQuant output
multiqc --maxquant-plugin /path/to/results -o ./report

# DIA-NN output
multiqc --diann-plugin /path/to/results -o ./report

# mzIdentML files
multiqc --mzid-plugin /path/to/results -o ./report

# ProteoBench result file
multiqc --proteobench-plugin /path/to/results -o ./report

# FragPipe output
multiqc --fragpipe-plugin /path/to/results -o ./report

# nf-core/mhcquant output
multiqc --mhcquant-plugin /path/to/results -o ./report

Plugin Selection Options¶

Option	Description	Default
`--quantms-plugin`	Enable the quantms module	`False`
`--maxquant-plugin`	Enable the MaxQuant module	`False`
`--diann-plugin`	Enable the DIA-NN module	`False`
`--mzid-plugin`	Enable the mzIdentML module	`False`
`--proteobench-plugin`	Enable the ProteoBench module	`False`
`--fragpipe-plugin`	Enable the FragPipe module	`False`
`--mhcquant-plugin`	Enable the mhcquant module	`False`

Identification Options¶

These options control how PSMs and peptides are counted and filtered.

Option	Description	Default
`--remove-decoy` / `--no-remove-decoy`	Remove decoy peptides from counts	`True` (remove)
`--decoy-affix TEXT`	Prefix or suffix identifying decoy proteins	`DECOY_`
`--contaminant-affix TEXT`	Prefix or suffix identifying contaminant proteins	`CONT`
`--affix-type [prefix\\|suffix]`	Whether the decoy/contaminant affix is a prefix or suffix	`prefix`

Example: if your search used REV_ as a decoy suffix:

multiqc --quantms-plugin results/ -o report/ \
  --decoy-affix REV_ --affix-type suffix

Quantification Options¶

Option	Description	Default
`--quantification-method [feature_intensity\\|spectral_counting]`	LFQ quantification method	`feature_intensity`
`--condition TEXT`	Column name to use for condition grouping (e.g., SDRF factor column)	—
`--keep-raw`	Keep raw filenames in the experimental design output table	`False`

Example: create conditions from an SDRF factor column:

multiqc --quantms-plugin results/ -o report/ \
  --condition "factor value[disease]"

Performance Options¶

Option	Description	Default
`--disable-table`	Skip rendering protein and peptide tables (recommended for >100 samples)	`False`
`--ignored-idxml`	Skip parsing idXML files (faster for large quantms outputs)	`False`

Display Options¶

Option	Description	Default
`--disable-hoverinfo`	Disable interactive hover tooltips on all plots	`False`

Use --disable-hoverinfo when generating static reports for PDF export or archiving.

Versioning¶

# Print the pmultiqc version
multiqc --pmultiqc-version

Standard MultiQC Options¶

pmultiqc inherits all standard MultiQC options. Commonly used ones in proteomics workflows:

# Set report title
multiqc --quantms-plugin results/ -o report/ --title "PXD012345 LFQ QC"

# Set report filename
multiqc --quantms-plugin results/ -o report/ --filename my_report.html

# Force overwrite of existing report
multiqc --quantms-plugin results/ -o report/ --force

# Verbose logging
multiqc --quantms-plugin results/ -o report/ --verbose

# Limit search depth to avoid scanning irrelevant subdirectories
multiqc --quantms-plugin results/ -o report/ --dirs-depth 2

Refer to the MultiQC documentation for the full list of standard options.