From 2a9fb02a3a2c26d2c95ebdd52d55f9d28af0bc58 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Wed, 20 Mar 2024 09:48:35 +0100
Subject: [PATCH] Fix duplicate citation entries

---
 assets/methods_description_template.yml       | 16 +-----------
 .../main.nf                                   | 26 +++++++++++--------
 2 files changed, 16 insertions(+), 26 deletions(-)

diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml
index a18700e..c65a0c4 100644
--- a/assets/methods_description_template.yml
+++ b/assets/methods_description_template.yml
@@ -11,21 +11,7 @@ data: |
   <pre><code>${workflow.commandLine}</code></pre>
   <p>${tool_citations}</p>
   <h4>References</h4>
-  <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
-    <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>
-    ${tool_bibliography}
-  </ul>
+  <ul>${tool_bibliography}</ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>
     <ul>
diff --git a/subworkflows/local/utils_nfcore_spatialtranscriptomics_pipeline/main.nf b/subworkflows/local/utils_nfcore_spatialtranscriptomics_pipeline/main.nf
index 90f1e6a..c037da1 100644
--- a/subworkflows/local/utils_nfcore_spatialtranscriptomics_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_spatialtranscriptomics_pipeline/main.nf
@@ -132,8 +132,9 @@ def toolCitationText() {
             "MultiQC (Ewels et al. 2016),",
             "Quarto (Allaire et al. 2022),",
             "Scanpy (Wolf et al. 2018),",
-            "Space Ranger (10x Genomics) and",
-            "SpatialDE (Svensson et al. 2018)."
+            "Space Ranger (10x Genomics)",
+            "SpatialData (Marconato et al. 2023) and",
+            "Squidpy (Palla et al. 2022)"
         ].join(' ').trim()
 
     return citation_text
@@ -142,13 +143,18 @@ def toolCitationText() {
 def toolBibliographyText() {
 
     def reference_text = [
-            "<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, URL: <a href=https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>bioinformatics.babraham.ac.uk</a>.</li>",
-            "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. 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, URL: <a href=https://www.10xgenomics.com/support/software/space-ranger>10xgenomics.com/support/software/space-ranger</a></li>",
-            "<li>Svensson V, Teichmann S, Stegle O. SpatialDE: identification of spatially variable genes. Nat Methods 15, 343–346 (2018). doi: <a href=https://doi.org/10.1038/nmeth.4636>10.1038/nmeth.4636</a></li>",
+        '<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>',
+        '<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>',
         ].join(' ').trim()
 
     return reference_text
@@ -165,8 +171,6 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["nodoi_text"] = meta.manifest_map.doi ? "": "<li>If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. </li>"
 
     // Tool references
-    meta["tool_citations"] = ""
-    meta["tool_bibliography"] = ""
     meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
     meta["tool_bibliography"] = toolBibliographyText()