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prettier and small fixes
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kubranarci committed Jan 24, 2024
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68 changes: 32 additions & 36 deletions README.md

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167 changes: 124 additions & 43 deletions assets/email_template.html
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<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">
<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 name="description" content="nf-core/aceseq: ACEseq Allele-specific copy number estimation with whole genome sequencing ODCF pipeline">
<title>nf-core/aceseq Pipeline Report</title>
</head>
<body>
<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
<meta
name="description"
content="nf-core/aceseq: ACEseq Allele-specific copy number estimation with whole genome sequencing ODCF pipeline"
/>
<title>nf-core/aceseq 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" />

<img src="cid:nfcorepipelinelogo">
<h1>nf-core/aceseq v${version}</h1>
<h2>Run Name: $runName</h2>

<h1>nf-core/aceseq 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/aceseq execution completed unsuccessfully!</h4>
<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
<% if (!success){ out << """
<div
style="
color: #a94442;
background-color: #f2dede;
border-color: #ebccd1;
padding: 15px;
margin-bottom: 20px;
border: 1px solid transparent;
border-radius: 4px;
"
>
<h4 style="margin-top: 0; color: inherit">
nf-core/aceseq execution completed unsuccessfully!
</h4>
<p>
The exit status of the task that caused the workflow execution to fail
was: <code>$exitStatus</code>.
</p>
<p>The full error message was:</p>
<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
</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;">
<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;
"
>
nf-core/aceseq execution completed successfully!
</div>
"""
}
%>
</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;">$commandLine</pre>
<p>
The workflow was completed at <strong>$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
>

<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") %>
</tbody>
</table>
<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") %>
</tbody>
</table>

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

</div>

</body>
<p>nf-core/aceseq</p>
<p>
<a href="https://github.com/nf-core/aceseq"
>https://github.com/nf-core/aceseq</a
>
</p>
</div>
</body>
</html>
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