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…re/quantms into nf-core-nf-core-template-merge-2.6
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email_template.html | ||
adaptivecard.json | ||
.nextflow* | ||
work/ | ||
data/ | ||
|
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{ | ||
"type": "message", | ||
"attachments": [ | ||
{ | ||
"contentType": "application/vnd.microsoft.card.adaptive", | ||
"contentUrl": null, | ||
"content": { | ||
"\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", | ||
"msteams": { | ||
"width": "Full" | ||
}, | ||
"type": "AdaptiveCard", | ||
"version": "1.2", | ||
"body": [ | ||
{ | ||
"type": "TextBlock", | ||
"size": "Large", | ||
"weight": "Bolder", | ||
"color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", | ||
"text": "nf-core/quantms v${version} - ${runName}", | ||
"wrap": true | ||
}, | ||
{ | ||
"type": "TextBlock", | ||
"spacing": "None", | ||
"text": "Completed at ${dateComplete} (duration: ${duration})", | ||
"isSubtle": true, | ||
"wrap": true | ||
}, | ||
{ | ||
"type": "TextBlock", | ||
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", | ||
"wrap": true | ||
}, | ||
{ | ||
"type": "TextBlock", | ||
"text": "The command used to launch the workflow was as follows:", | ||
"wrap": true | ||
}, | ||
{ | ||
"type": "TextBlock", | ||
"text": "${commandLine}", | ||
"isSubtle": true, | ||
"wrap": true | ||
} | ||
], | ||
"actions": [ | ||
{ | ||
"type": "Action.ShowCard", | ||
"title": "Pipeline Configuration", | ||
"card": { | ||
"type": "AdaptiveCard", | ||
"\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", | ||
"body": [ | ||
{ | ||
"type": "FactSet", | ||
"facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> | ||
] | ||
} | ||
] | ||
} | ||
} | ||
] | ||
} | ||
} | ||
] | ||
} |
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id: "nf-core-quantms-methods-description" | ||
description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." | ||
section_name: "nf-core/quantms Methods Description" | ||
section_href: "https://github.com/nf-core/quantms" | ||
plot_type: "html" | ||
## 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 '${workflow}' object | ||
data: | | ||
<h4>Methods</h4> | ||
<p>Data was processed using nf-core/quantms v${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> | ||
<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> |
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8 changes: 4 additions & 4 deletions
8
...dules/custom/dumpsoftwareversions/main.nf → ...-core/custom/dumpsoftwareversions/main.nf
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15 changes: 15 additions & 0 deletions
15
modules/nf-core/modules/multiqc/meta.yml → modules/nf-core/multiqc/meta.yml
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