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25 lines
2 KiB
YAML
25 lines
2 KiB
YAML
id: "nf-core-taxprofiler-methods-description"
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description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
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section_name: "nf-core/taxprofiler Methods Description"
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section_href: "https://github.com/nf-core/taxprofiler"
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plot_type: "html"
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## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>
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<p>Data was processed using nf-core/taxprofiler v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
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<p>The pipeline was executed with Nextflow v${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>
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<pre><code>${workflow.commandLine}</code></pre>
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<h4>References</h4>
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<ul>
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<li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
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<li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
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</ul>
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<div class="alert alert-info">
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<h5>Notes:</h5>
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<ul>
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${nodoi_text}
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<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>
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<li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
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</ul>
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</div>
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