add DOI and CITATION.cff

CITATION.cff

@@ -0,0 +1,41 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: >-
+  Single-cell RNA sequencing (scRNA-seq) Data Processing &
+  Visualization Workflow
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Stephan
+    family-names: Reichl
+    orcid: 'https://orcid.org/0000-0001-8555-7198'
+    affiliation: CeMM Research Center for Molecular Medicine
+  - given-names: Christoph
+    family-names: Bock
+    orcid: 'https://orcid.org/0000-0001-6091-3088'
+    affiliation: CeMM Research Center for Molecular Medicine
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.10679327
+    description: >-
+      This DOI represents all versions, and will always
+      resolve to the latest one.
+repository-code: 'https://github.com/epigen/scrnaseq_processing_seurat/'
+url: 'https://epigen.github.io/scrnaseq_processing_seurat/'
+abstract: >-
+  A Snakemake workflow for processing and visualizing
+  (multimodal) sc/snRNA-seq data generated with 10X Genomics
+  Kits or in the MTX matrix file format powered by the R
+  package Seurat.
+keywords:
+  - scRNA-seq
+  - Visualization
+  - Multimodal
+  - Bioinformatics
+  - Workflow
+  - Snakemake
+license: MIT

README.md

@@ -1,3 +1,5 @@
+[![DOI](https://zenodo.org/badge/468752490.svg)](https://zenodo.org/doi/10.5281/zenodo.10679327)
+
 # Single-cell RNA sequencing (scRNA-seq) Data Processing & Visualization Snakemake Workflow
 
 sc/snRNA-seq Data Processing & Visualization Snakemake Workflow powered by Seurat
@@ -8,6 +10,8 @@ This workflow adheres to the module specifications of [MR.PARETO](https://github
 
 **If you use this workflow in a publication, don't forget to give credits to the authors by citing the URL of this (original) repository (and its DOI, see Zenodo badge above -> coming soon).**
 
+**If you use this workflow in a publication, please don't forget to give credits to the authors by citing it using this DOI [10.5281/zenodo.10679327](https://zenodo.org/doi/10.5281/zenodo.10679327).**
+
 ![Workflow Rulegraph](./workflow/dags/rulegraph.svg)
 
 Table of contents
@@ -65,7 +69,7 @@ The outlined analyses were performed using the R package Seurat (ver) [ref] unle
 
 **Visualization.** To visualize the metadata after each processing step inspectdf (ver) [ref] was used. For the visualization of expression, multimodal [X] data and calculated metadata like module scores, the Seurat functions RidgePlot for ridge plots, VlnPlot for violin plots, DotPlot for dot plots and DoHeatmap for heatmaps were used.
 
-**The processing, analysis and visualizations described here were performed using a publicly available Snakemake [ver] (ref) workflow [ref - cite this workflow here].**
+**The processing, analysis and visualizations described here were performed using a publicly available Snakemake [ver] (ref) workflow [[10.5281/zenodo.10679327](https://zenodo.org/doi/10.5281/zenodo.10679327)].**
 
 
 # Features
@@ -186,7 +190,7 @@ Beyond this the workflow was tested on multimodal scCRISPR-seq data sets with >3
 # Links
 - [GitHub Repository](https://github.com/epigen/scrnaseq_processing_seurat/)
 - [GitHub Page](https://epigen.github.io/scrnaseq_processing_seurat/)
-- [Zenodo Repository (coming soon)]()
+- [Zenodo Repository](https://zenodo.org/doi/10.5281/zenodo.10679327)
 - [Snakemake Workflow Catalog Entry](https://snakemake.github.io/snakemake-workflow-catalog?usage=epigen/scrnaseq_processing_seurat)
 
 # Resources