chore: define parameters in config readme.

Author: rabioinf

config/README.md

@@ -20,5 +20,36 @@ The samplesheet table has the following layout:
 | sample | species                  | strain | id_prefix | file           |
 | ------ | ------------------------ | ------ | --------- | -------------- |
 | EC2224 | "Streptococcus pyogenes" | SF370  | SPY       | assembly.fasta |
+| ...    | ...                      | ...    | ...       | ...            |
 
-**Note:** Pangenome analysis with `Panaroo` requires at least two samples.
+**Note:** Pangenome analysis with `Panaroo` requires at least two samples.
+
+### Parameters
+
+This table lists all parameters that can be used to run the workflow.
+
+| Parameter | Type | Details | Default |
+|:---|:---|:---|:---|
+| **samplesheet** | string | Path to the sample sheet file in csv format | |
+| **tool** | array[string] | Annotation tool to use (one of `prokka`, `pgap`, `bakta`) | |
+| **pgap** | | PGAP configuration object |  |
+| bin | string | Path to the PGAP script | |
+| use_yaml_config | boolean | Whether to use YAML configuration for PGAP | `False` |
+| _prepare_yaml_files_ | | Paths to YAML templates for PGAP | |
+| generic | string | Path to the generic YAML configuration file | |
+| submol | string | Path to the submol YAML configuration file | |
+| **prokka** | | Prokka configuration object | |
+| center | string | Center name for Prokka annotation (used in sequence IDs) | |
+| extra | string | Extra command-line arguments for Prokka | |
+| **bakta** | | Bakta configuration object | |
+| download_db | string | Bakta database type (`full`, `light`, or `none`) | `light` |
+| existing_db | string | Path to an existing Bakta database (optional). Needs to be combined with `download_db='none'` | |
+| extra | string | Extra command-line arguments for Bakta | |
+| **quast** | | QUAST configuration object | |
+| reference_fasta | string | Path to the reference genome for QUAST | |
+| reference_gff | string | Path to the reference annotation for QUAST |
+| extra | string | Extra command-line arguments for QUAST | |
+| **panaroo** | | Panaroo configuration object | |
+| remove_source | string | Source types to remove in Panaroo (regex supported) | `cmsearch` |
+| remove_feature | string | Feature types to remove in Panaroo (regex supported) | `tRNA\|rRNA\|ncRNA\|exon\|sequence_feature` |
+| extra | string | Extra command-line arguments for Panaroo | |