Skip to content

Commit

Permalink
Fix duplicate citation entries
Browse files Browse the repository at this point in the history
  • Loading branch information
@fasterius
fasterius committed Mar 20, 2024
1 parent 354f3af commit 2a9fb02
Show file tree
Hide file tree
Showing 2 changed files with 16 additions and 26 deletions.
16 changes: 1 addition & 15 deletions assets/methods_description_template.yml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
26 changes: 15 additions & 11 deletions subworkflows/local/utils_nfcore_spatialtranscriptomics_pipeline/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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()

Expand Down

0 comments on commit 2a9fb02

Please sign in to comment.