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Merge pull request #211 from nf-core/dev
PR for release 2.4.0
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,4 +1,5 @@ | ||
| email_template.html | ||
| adaptivecard.json | ||
| .nextflow* | ||
| work/ | ||
| data/ | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| { | ||
| "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/airrflow 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| id: "nf-core-airrflow-methods-description" | ||
| description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." | ||
| section_name: "nf-core/airrflow Methods Description" | ||
| section_href: "https://github.com/nf-core/airrflow" | ||
| 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 '${workflow}' object | ||
| data: | | ||
| <h4>Methods</h4> | ||
| <p>Data was processed using nf-core/airrflow v${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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