| Category | Parameter | Description | Default Value |
|---|---|---|---|
| Input/output options | input | Path to input data file. | - |
| outdir | Path to the directory where the results will be saved. | - | |
| Email address for receiving completion notification. | - | ||
| multiqc_title | Title for the MultiQC report. | - | |
| Reference genome options | igenomes_ignore | Flag to ignore iGenomes reference configuration. | - |
| fasta | Path to the reference genome FASTA file. | - | |
| adapterlist | Path to the adapter list file. | - | |
| Skip options | skip_preprocessing | Skip preprocessing step. | - |
| skip_qualityfilter | Skip quality filtering step. | - | |
| skip_humanfilter | Skip human filtering step. | - | |
| skip_subsampling | Skip subsampling step. | - | |
| skip_metaphlan | Skip MetaPhlAn analysis. | - | |
| skip_humann | Skip HUMAnN analysis. | - | |
| skip_strainphlan | Skip StrainPhlAn analysis. | true | |
| Preprocessing of reads | save_trimmed_fail | Save trimmed reads that fail filtering. | - |
| fastp_cutright | Perform trimming from the right end. | true | |
| fastp_windowsize | Window size for quality filtering in Fastp. | 4 | |
| fastp_meanquality | Mean quality threshold for filtering in Fastp. | 15 | |
| fastp_length | Minimum length threshold for reads in Fastp. | 70 | |
| subsamplelevel | Level of subsampling for reads. | 20000000 | |
| HUMAnN | database | Database to use for HUMAnN analysis. | - |
| StrainPhlAn | phylophlan_mode | PhyloPhlAn mode for analysis. | accurate |
| sample_with_n_markers | Minimum number of markers in a sample for StrainPhlAn. | 80 | |
| marker_in_n_samples | Minimum number of samples containing a marker for StrainPhlAn. | 80 | |
| mutation_rates | Include mutation rates in StrainPhlAn analysis. | true |