Updated configs (31fb853e) · Commits · Chaos / Cutandrun

.nf-core.yml

+0 −6

Original line number	Diff line number	Diff line
		@@ -5,9 +5,3 @@ lint:
		- assets/email_template.html
		- assets/email_template.txt
		- lib/NfcoreTemplate.groovy
		- .github/ISSUE_TEMPLATE/bug_report.yml
		- .github/PULL_REQUEST_TEMPLATE.md
		- .github/workflows/branch.yml
		- .github/workflows/linting_comment.yml
		- .github/workflows/linting.yml
		- lib/NfcoreSchema.groovy

assets/email_template.html

+43 −101

Original line number	Diff line number	Diff line
		<html>
		<head>
		<meta charset="utf-8" />
		<meta http-equiv="X-UA-Compatible" content="IE=edge" />
		<meta name="viewport" content="width=device-width, initial-scale=1" />
		<meta charset="utf-8">
		<meta http-equiv="X-UA-Compatible" content="IE=edge">
		<meta name="viewport" content="width=device-width, initial-scale=1">

		<!-- prettier-ignore -->
		<meta name="description" content="nf-core/cutandrun: Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis." />
		<meta name="description" content="nf-core/cutandrun: Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.">
		<title>nf-core/cutandrun Pipeline Report</title>
		</head>
		<body>
		<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
		<img src="cid:nfcorepipelinelogo" />
		<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">

		<img src="cid:nfcorepipelinelogo">

		<h1>nf-core/cutandrun v${version}</h1>
		<h2>Run Name: $runName</h2>

		<% if (!success){ out << """
		<div
		style="
		color: #a94442;
		background-color: #f2dede;
		border-color: #ebccd1;
		padding: 15px;
		margin-bottom: 20px;
		border: 1px solid transparent;
		border-radius: 4px;
		"
		>
		<h4 style="margin-top: 0; color: inherit">nf-core/cutandrun execution completed unsuccessfully!</h4>
		<% if (!success){
		out << """
		<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
		<h4 style="margin-top:0; color: inherit;">nf-core/cutandrun execution completed unsuccessfully!</h4>
		<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
		<p>The full error message was:</p>
		<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
		<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
		</div>
		""" } else { out << """
		<div
		style="
		color: #3c763d;
		background-color: #dff0d8;
		border-color: #d6e9c6;
		padding: 15px;
		margin-bottom: 20px;
		border: 1px solid transparent;
		border-radius: 4px;
		"
		>
		"""
		} else {
		out << """
		<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
		nf-core/cutandrun execution completed successfully!
		</div>
		""" } %>
		"""
		}
		%>

		<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
		<p>The command used to launch the workflow was as follows:</p>
		<pre
		style="
		white-space: pre-wrap;
		overflow: visible;
		background-color: #ededed;
		padding: 15px;
		border-radius: 4px;
		margin-bottom: 30px;
		"
		>
		$commandLine</pre
		>
		<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>

		<h3>Pipeline Configuration:</h3>
		<table
		style="
		width: 100%;
		max-width: 100%;
		border-spacing: 0;
		border-collapse: collapse;
		border: 0;
		margin-bottom: 30px;
		"
		>
		<tbody style="border-bottom: 1px solid #ddd">
		<% out << summary.collect{ k,v -> "
		<tr>
		<th
		style="
		text-align: left;
		padding: 8px 0;
		line-height: 1.42857143;
		vertical-align: top;
		border-top: 1px solid #ddd;
		"
		>
		$k
		</th>
		<td
		style="
		text-align: left;
		padding: 8px;
		line-height: 1.42857143;
		vertical-align: top;
		border-top: 1px solid #ddd;
		"
		>
		<pre style="white-space: pre-wrap; overflow: visible">$v</pre>
		</td>
		</tr>
		" }.join("\n") %>
		<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
		<tbody style="border-bottom: 1px solid #ddd;">
		<% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %>
		</tbody>
		</table>

		<p>nf-core/cutandrun</p>
		<p><a href="https://github.com/nf-core/cutandrun">https://github.com/nf-core/cutandrun</a></p>

		</div>

		</body>
		</html>
		No newline at end of file

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