id: "nf-core-ampliseq-methods-description"
description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
section_name: "nf-core/ampliseq Methods Description"
section_href: "https://github.com/nf-core/ampliseq"
plot_type: "html"
## 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 '${workflow}' object
data: |
  <h4>Methods</h4>
  <p>Data was processed using nf-core/ampliseq v${workflow.manifest.version} ${doi_text} (<a href="https://doi.org/10.3389/fmicb.2020.550420">Straub <em>et al.</em>, 2020</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
  <p>The pipeline was executed with Nextflow v${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>
  <h4>References</h4>
  <ul>
    <li>Straub D, Blackwell N, Langarica-Fuentes A, Peltzer A, Nahnsen S, Kleindienst S. Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Front Microbiol. 2020 Oct 23;11:550420. <a href="https://doi.org/10.3389/fmicb.2020.550420">https://doi.org/10.3389/fmicb.2020.550420</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>
    ${tool_bibliography}
  </ul>
  <div class="alert alert-info">
    <h5>Notes:</h5>
    <ul>
      ${nodoi_text}
      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
    </ul>
  </div>
