add preprint citation

README.md

@@ -144,11 +144,17 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/airrflow was written by [Gisela Gabernet](https://github.com/ggabernet), [Susanna Marquez](https://github.com/ssnn-airr), [Alexander Peltzer](@apeltzer) and [Simon Heumos](@subwaystation).
+nf-core/airrflow was originally written by:
 
-Further contributors to the pipeline are:
+- [Gisela Gabernet](https://github.com/ggabernet)
+- [Susanna Marquez](https://github.com/ssnn-airr)
+- [Alexander Peltzer](@apeltzer)
+- [Simon Heumos](@subwaystation)
 
-- [@dladd](https://github.com/dladd)
+We thank the following people for their extensive assistance in the development of the pipeline:
+
+- [David Ladd](https://github.com/dladd)
+- [Friederike Hanssen](https://github.com/ggabernet/friederikehanssen)
 
 ## Contributions and Support
 
@@ -158,9 +164,17 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use nf-core/airrflow for your analysis, please cite it using the following DOI: [10.5281/zenodo.2642009](https://doi.org/10.5281/zenodo.2642009)
+If you use nf-core/airrflow for your analysis, please cite the preprint as follows:
+
+> **nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework**
+>
+> Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole Jensen, David Ladd, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein.
+>
+> BioRxiv. 2024. doi: [10.1101/2024.01.18.576147](https://doi.org/10.1101/2024.01.18.576147).
+
+The specific pipeline version it using the following DOI: [10.5281/zenodo.2642009](https://doi.org/10.5281/zenodo.2642009)
 
-An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+Please also cite all the tools that are being used by the pipeline. An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:
 

assets/methods_description_template.yml

@@ -3,11 +3,9 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/airrflow Methods Description"
 section_href: "https://github.com/nf-core/airrflow"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
-## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-core/airrflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
+  <p>Data was processed using nf-core/airrflow v${workflow.manifest.version} (${doi_text}; <a href="https://doi.org/10.1101/2024.01.18.576147">Gabernet <em>et al.</em>, 2024</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>