cleanup

README.md

@@ -1,6 +1,5 @@
 [![Super-Linter](https://github.com/JohannesGawron/CTC-SCITE/actions/workflows/linter.yml/badge.svg)](https://github.com/marketplace/actions/super-linter)
-[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0-brightgreen.svg)](https://snakemake.github.io) 
-[![Code style: snakefmt](https://img.shields.io/badge/code%20style-snakefmt-000000.svg)](https://github.com/snakemake/snakefmt)
+
 
 
 # Interrogating the clonality of circulating tumor cell (CTC) clusters

experiments/assessing_cluster_clonality/README.md

@@ -1,13 +1,22 @@
+[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0-brightgreen.svg)](https://snakemake.github.io)
+[![Code style: snakefmt](https://img.shields.io/badge/code%20style-snakefmt-000000.svg)](https://github.com/snakemake/snakefmt)
+
 # Snakemake workflow for full reproducibility of the project
+============================================================
 
 ## Description
+--------------
+
+This directory contains the code executed to perform the interrogation of clonality of CTC clusters. To facilitate full reproducibility, it has been implemented as a **snakemake** workflow. Some code for one-time manual manipulation of the data can be found in the subdirectory `sandbox/`.
+
+
 ## Usage
-Run
-`snakemake --configfile config/config.yaml --cores 4 --use-conda`
+--------
 
+The pipeline is implemented in snakemake 8. For the installation, please follow the [official documentation](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html 'Snakemake docs')
 
-To run the workflow, run `snakemake`
+To rerun the analysis, navigate to this directory in the terminal and run
 
-If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).
+`snakemake --configfile config/config.yaml --cores 4 --use-conda`
 
 Owner: Johannes Gawron