Template update for nf-core/tools version 2.3.1
nf-core-bot
2 years ago
parent
699d26b149
commit
6b939e6728
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# Markdownlint configuration file
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default: true
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line-length: false
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ul-indent:
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indent: 4
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no-duplicate-header:
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siblings_only: true
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no-inline-html:
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allowed_elements:
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- img
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- p
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- kbd
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- details
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- summary
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@ -0,0 +1 @@
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printWidth: 120
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@ -1,6 +0,0 @@
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extends: default
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rules:
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document-start: disable
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line-length: disable
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truthy: disable
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@ -1,53 +1,111 @@
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<html>
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<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<head>
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<meta charset="utf-8" />
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<meta http-equiv="X-UA-Compatible" content="IE=edge" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data">
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<title>nf-core/taxprofiler Pipeline Report</title>
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</head>
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<body>
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<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;">
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<!-- prettier-ignore -->
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<meta name="description" content="nf-core/taxprofiler: Taxonomic profiling of shotgun metagenomic data" />
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<title>nf-core/taxprofiler Pipeline Report</title>
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</head>
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<body>
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<div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
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<img src="cid:nfcorepipelinelogo" />
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<img src="cid:nfcorepipelinelogo">
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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<% if (!success){
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out << """
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<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
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<h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<% if (!success){ out << """
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<div
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style="
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color: #a94442;
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background-color: #f2dede;
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border-color: #ebccd1;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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<h4 style="margin-top: 0; color: inherit">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
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<p>The full error message was:</p>
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<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
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</div>
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"""
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} else {
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out << """
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<div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
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<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
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</div>
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""" } else { out << """
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<div
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style="
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color: #3c763d;
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background-color: #dff0d8;
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border-color: #d6e9c6;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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nf-core/taxprofiler execution completed successfully!
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</div>
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"""
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}
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%>
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</div>
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""" } %>
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<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
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<p>The command used to launch the workflow was as follows:</p>
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<pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre>
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<p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
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<p>The command used to launch the workflow was as follows:</p>
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<pre
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style="
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white-space: pre-wrap;
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overflow: visible;
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background-color: #ededed;
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padding: 15px;
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border-radius: 4px;
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margin-bottom: 30px;
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"
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>
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$commandLine</pre
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>
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<h3>Pipeline Configuration:</h3>
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<table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;">
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<tbody style="border-bottom: 1px solid #ddd;">
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<% 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") %>
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</tbody>
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</table>
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<h3>Pipeline Configuration:</h3>
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<table
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style="
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width: 100%;
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max-width: 100%;
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border-spacing: 0;
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border-collapse: collapse;
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border: 0;
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margin-bottom: 30px;
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"
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>
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<tbody style="border-bottom: 1px solid #ddd">
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<% out << summary.collect{ k,v -> "
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<tr>
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<th
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style="
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text-align: left;
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padding: 8px 0;
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line-height: 1.42857143;
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vertical-align: top;
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border-top: 1px solid #ddd;
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"
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>
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$k
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</th>
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<td
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style="
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text-align: left;
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padding: 8px;
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line-height: 1.42857143;
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vertical-align: top;
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border-top: 1px solid #ddd;
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"
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>
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<pre style="white-space: pre-wrap; overflow: visible">$v</pre>
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</td>
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</tr>
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" }.join("\n") %>
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</tbody>
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</table>
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<p>nf-core/taxprofiler</p>
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<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
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</div>
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</body>
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<p>nf-core/taxprofiler</p>
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<p><a href="https://github.com/nf-core/taxprofiler">https://github.com/nf-core/taxprofiler</a></p>
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</div>
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</body>
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</html>
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/taxprofiler" target="_blank">nf-core/taxprofiler</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
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report_section_order:
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software_versions:
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order: -1000
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nf-core-taxprofiler-summary:
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order: -1001
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export_plots: true
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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/taxprofiler" target="_blank">nf-core/taxprofiler</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
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report_section_order:
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software_versions:
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order: -1000
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"nf-core-taxprofiler-summary":
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order: -1001
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export_plots: true
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name: fastqc
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description: Run FastQC on sequenced reads
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keywords:
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- quality control
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- qc
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- adapters
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- fastq
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- quality control
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- qc
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- adapters
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- fastq
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tools:
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- fastqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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licence: ['GPL-2.0-only']
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- fastqc:
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description: |
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FastQC gives general quality metrics about your reads.
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It provides information about the quality score distribution
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across your reads, the per base sequence content (%A/C/G/T).
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You get information about adapter contamination and other
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overrepresented sequences.
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homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
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documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
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licence: ["GPL-2.0-only"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- html:
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type: file
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description: FastQC report
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pattern: "*_{fastqc.html}"
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- zip:
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type: file
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description: FastQC report archive
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pattern: "*_{fastqc.zip}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- html:
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type: file
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description: FastQC report
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pattern: "*_{fastqc.html}"
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- zip:
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type: file
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description: FastQC report archive
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pattern: "*_{fastqc.zip}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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- "@grst"
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- "@ewels"
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- "@FelixKrueger"
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- "@drpatelh"
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- "@grst"
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- "@ewels"
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- "@FelixKrueger"
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name: MultiQC
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description: Aggregate results from bioinformatics analyses across many samples into a single report
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keywords:
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- QC
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- bioinformatics tools
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- Beautiful stand-alone HTML report
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- QC
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- bioinformatics tools
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- Beautiful stand-alone HTML report
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tools:
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- multiqc:
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description: |
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MultiQC searches a given directory for analysis logs and compiles a HTML report.
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It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
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homepage: https://multiqc.info/
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documentation: https://multiqc.info/docs/
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licence: ['GPL-3.0-or-later']
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- multiqc:
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description: |
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MultiQC searches a given directory for analysis logs and compiles a HTML report.
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It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
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homepage: https://multiqc.info/
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documentation: https://multiqc.info/docs/
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licence: ["GPL-3.0-or-later"]
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input:
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- multiqc_files:
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type: file
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description: |
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List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
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- multiqc_files:
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type: file
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description: |
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List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
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output:
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- report:
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type: file
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description: MultiQC report file
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pattern: "multiqc_report.html"
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- data:
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type: dir
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description: MultiQC data dir
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pattern: "multiqc_data"
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- plots:
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type: file
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description: Plots created by MultiQC
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pattern: "*_data"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- report:
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type: file
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description: MultiQC report file
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pattern: "multiqc_report.html"
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- data:
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type: dir
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description: MultiQC data dir
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pattern: "multiqc_data"
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- plots:
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type: file
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description: Plots created by MultiQC
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pattern: "*_data"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@abhi18av"
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- "@bunop"
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- "@drpatelh"
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- "@abhi18av"
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- "@bunop"
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- "@drpatelh"
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