Perform label-free quantification using Philosopher's freequant command.
FreeQuant extracts ion intensity information from mass spectrometry data files to quantify peptide and protein abundances.
It initializes a Philosopher workspace in the results directory, runs FreeQuant with the provided CLI config, and preserves the .meta/ workspace for downstream PHILOSOPHERREPORT.
Used within the FRAGPIPE_QUANT subworkflow as an alternative to IonQuant for label-free quantification.
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Sample metadata map |
| results_dir | path | Directory containing psm.tsv from PHILOSOPHERFILTER |
| mzml_dir | path | Directory containing mass spectrometry files (mzML or RAW) |
| config_cli | val(string) | FreeQuant parameters as CLI string (e.g., --ptw 0.4 --tol 10) |
| Channel | Type | Description |
|---|---|---|
| results_dir | tuple(meta, path) | Output directory with results and .meta/ workspace |
| ions | tuple(meta, path) | Ion-level quantification results (ion.tsv, optional) |
| versions_philosopher | tuple | Philosopher software version (topic channel) |
| versions_fragpipe | tuple | FragPipe software version (topic channel) |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional CLI arguments appended to the philosopher freequant command |
| ext.prefix | meta.id | Override for the output directory name |
| ext.fragpipe_tools_dir | (auto-detected) | Override for the FragPipe tools directory path |
The licensed FragPipe image given with --fragpipe_container.
Used in the FRAGPIPE_QUANT subworkflow (subworkflows/local/fragpipe_quant/main.nf) for label-free ion intensity quantification.
Automatically detects .raw files and adds the --raw flag.