chore: Add config instructions in extra README file

README.md

@@ -3,7 +3,6 @@
 Author: [email protected]
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥8.10.0-brightgreen.svg)](https://snakemake.github.io)
-[![GitHub actions status](https://github.com/basecallNanopore/basecallNanopore/workflows/Tests/badge.svg?branch=main)](https://github.com/richardstoeckl/basecallNanopore/actions?query=branch%3Amain+workflow%3ATests)
 
 ## About
 
@@ -31,6 +30,10 @@ For Dorado, a pipeline based on [recommendations from Nanopore](https://github.c
 3. Basecall using Dorado in duplex mode but constrain to the reads for each barcode seperately
 
 ## Usage
+
+**[Check out the usage instructions in the snakemake workflow catalog](https://snakemake.github.io/snakemake-workflow-catalog?usage=richardstoeckl/basecallNanopore)**
+
+But here is a rough overview:
 1. Install [conda](https://docs.conda.io/en/latest/miniconda.html) (mamba or miniconda is fine).
 2. Install snakemake with:
 ```bash

config/README.md

@@ -0,0 +1,22 @@
+# General configuration
+
+To configure this workflow, modify `config/config.yaml` according to your needs, following the explanations provided in the file.
+
+## "Main" section
+
+Here you should provide the paths to your intermediary/results/logs directories. The `interim` directory will contain larger intermediary files. The `results` directory will contain the final output of the pipeline. The `log`directory will be used to store the log files for each step.
+Here you should also write the name of your run file (see [relevant section below](#run-file-setup)).
+
+## "Tools" section
+
+Here you should give the paths to your guppy and/or dorado installation. Additionally you should change the given parameters to suit your compute setup.
+
+
+# Run file setup
+
+The setup of the basecall runs is specified via comma-separated values files (`.csv`).
+Missing values can be specified by empty columns.
+
+Depending on what you enter here, the pipeline will automatically adjust what will be done (e.g. which basecaller will be used and how many barcodes will be used).
+
+You can use the `config/runs_test.csv`file as a template.