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Update HTML to preferred methods description #197

Closed
Tracked by #200
sofstam opened this issue Dec 16, 2022 · 1 comment · Fixed by #308
Closed
Tracked by #200

Update HTML to preferred methods description #197

sofstam opened this issue Dec 16, 2022 · 1 comment · Fixed by #308
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enhancement Improvement for existing functionality low-priority

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@sofstam
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sofstam commented Dec 16, 2022

Description of feature

Going through ToDos before first-release and it would be nice to update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
## You inject any metadata in the Nextflow '${workflow}' object
data: |
<h4>Methods</h4>
<p>Data was processed using nf-core/taxprofiler v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
<p>The pipeline was executed with Nextflow v${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>
<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. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/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. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
</ul>
<div class="alert alert-info">
<h5>Notes:</h5>

@sofstam sofstam added enhancement Improvement for existing functionality low-priority labels Dec 16, 2022
@sofstam sofstam mentioned this issue Dec 16, 2022
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@jfy133 jfy133 modified the milestones: First Release, 1.1 Dec 20, 2022
@jfy133
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jfy133 commented Dec 20, 2022

Maybe we wait until the publication for this, and to giveme more time to see if we can dynamically include citation info for each tool (an idea I had for funcscan)

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