replace readme rst with md

README.md

@@ -0,0 +1,56 @@
+[![linux](https://github.com/maxplanck-ie/snakepipes/actions/workflows/linux.yml/badge.svg)](https://github.com/maxplanck-ie/snakepipes/actions/workflows/linux.yml)
+[![osx](https://github.com/maxplanck-ie/snakepipes/actions/workflows/osx.yml/badge.svg)](https://github.com/maxplanck-ie/snakepipes/actions/workflows/osx.yml)
+[![pytest](https://github.com/maxplanck-ie/snakepipes/actions/workflows/pytest.yml/badge.svg)](https://github.com/maxplanck-ie/snakepipes/actions/workflows/pytest.yml)
+[![readthedocs]](https://readthedocs.org/projects/snakepipes/badge/?version=latest)
+[![citation](https://zenodo.org/badge/54579435.svg)](https://zenodo.org/badge/latestdoi/54579435)
+
+# SnakePipes
+
+snakePipes are flexible and powerful workflows built using [snakemake](https://github.com/snakemake/snakemake) that simplify the analysis of NGS data.
+![snakePipes](.docs/content/images/snakePipes_small.png)
+
+## Workflows
+
+- DNAmapping*  
+- ChIPseq*  
+- mRNAseq*  
+- ncRNAseq*  
+- ATACseq*  
+- scRNAseq  
+- HiC  
+- makePairs*  
+- Whole Genome Bisulfite Seq/WGBS  
+
+(* also available in allele-specific mode)
+
+## Installation
+
+[Conda](https://docs.conda.io/en/latest/#) is a pre-requisite for snakePipes. So make sure this is [installed](https://conda.io/projects/conda/en/latest/user-guide/install/index.html) before.
+
+Afterwards you can create a snakePipes environment containing the installation by running:
+
+ > conda create -n snakepipes -c mpi-ie -c bioconda -c conda-forge snakePipes
+
+In case you'd like a development version, you can install snakePipes directly from github using pip:
+
+ > git clone [email protected]:maxplanck-ie/snakepipes.git  
+ > cd snakepipes
+ > pip install .
+
+Make sure the environment you are installing this version into has python version 3.11 or later.
+
+After the installation some configurations have to be set, for which we refer to the documentation.
+
+## Documentation
+
+For detailed documentation on setup and usage, please visit the [documentation](https://snakepipes.readthedocs.io/en/latest/).
+
+## Citation
+
+If you adopt/run snakePipes for your analysis, please cite it as follows :
+
+Bhardwaj, Vivek, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, and Thomas Manke. 2019. “snakePipes: Facilitating Flexible, Scalable and Integrative Epigenomic Analysis.” Bioinformatics , May. [doi:10.1093/bioinformatics/btz436](https://doi.org/10.1093/bioinformatics/btz436).
+
+## Note
+
+SnakePipes are under active development. We appreciate your help in improving it further. Please use issues to the GitHub repository for feature requests or bug reports.

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "snakePipes"
 description = 'Snakemake workflows and wrappers for NGS data processing from the MPI-IE'
-readme = "README.rst"
+readme = "README.md"
 version = "3.0.0"
 keywords = [
     "DNAmapping",