Update citations

CITATIONS.md

@@ -32,11 +32,15 @@
 
 - [Space Ranger](https://www.10xgenomics.com/support/software/space-ranger)
 
-  > 10x Genomics Space Ranger 2.1.0
+  > 10x Genomics Space Ranger 2.1.0 [Online]
 
-- [SpatialDE](https://github.com/Teichlab/SpatialDE)
+- [SpatialData](https://www.biorxiv.org/content/10.1101/2023.05.05.539647v1)
 
-  > Svensson V, Teichmann S, Stegle O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). doi: https://doi.org/10.1038/nmeth.4636
+  > Marconato L, Palla G, Yamauchi K, Virshup I, Heidari E, Treis T, Toth M, Shrestha R, Vöhringer H, Huber W, Gerstung M, Moore J, Theis F, Stegle O. SpatialData: an open and universal data framework for spatial omics. bioRxiv 2023.05.05.539647; doi: https://doi.org/10.1101/2023.05.05.539647
+
+- [Squipy](https://www.nature.com/articles/s41592-021-01358-2)
+
+  > Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: https://doi.org/10.1038/s41592-021-01358-2
 
 ## Software packaging/containerisation tools
 

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/spatialtranscriptomics Methods Description"
 section_href: "https://github.com/nf-core/spatialtranscriptomics"
 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>
@@ -17,6 +16,14 @@ data: |
     <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
     <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
     <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    <li> Virshup I, Rybakov S, Theis FJ, Angerer P, Wolf FA. bioRxiv 2021.12.16.473007. doi: <a href="https://doi.org/10.1101/2021.12.16.473007">10.1101/2021.12.16.473007</a></li>
+    <li>Andrews S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]: <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/">bioinformatics.babraham.ak.uk/project/fastqc</a></li>
+    <li>Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. doi: <a href="https://doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>
+    <li>Allaire J, Teague C, Scheidegger C, Xie Y, Dervieux C. Quarto (2022). doi: <a href="https://doi.org/10.5281/zenodo.5960048">10.5281/zenodo.5960048</a></li>
+    <li>Wolf F, Angerer P, Theis F. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol 19, 15 (2018). doi: <a href="https://doi.org/10.1186/s13059-017-1382-0">10.1186/s13059-017-1382-0</a></li>
+    <li>10x Genomics Space Ranger 2.1.0 [Online]<a href="https://www.10xgenomics.com/support/software/space-ranger">10xgenomics.com/support/software/space-ranger</a></li>
+    <li>Marconato L, Palla G, Yamauchi K, Virshup I, Heidari E, Treis T, Toth M, Shrestha R, Vöhringer H, Huber W, Gerstung M, Moore J, Theis F, Stegle O. SpatialData: an open and universal data framework for spatial omics. bioRxiv 2023.05.05.539647; doi:<a href="https://doi.org/10.1101/2023.05.05.539647"> 10.1101/2023.05.05.539647</a></li>
+    <li>Palla G, Spitzer H, Klein M et al. Squidpy: a scalable framework for spatial omics analysis. Nat Methods 19, 171–178 (2022). doi: <a href="https://doi.org/10.1038/s41592-021-01358-2">10.1038/s41592-021-01358-2</a></li>
     ${tool_bibliography}
   </ul>
   <div class="alert alert-info">