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First implementation of lofreq and bedtools
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AitorOP
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Aug 12, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,14 @@ | ||
| # Ignore artifacts: | ||
| build | ||
| coverage | ||
| email_template.html | ||
| adaptivecard.json | ||
| slackreport.json | ||
| .nextflow* | ||
| work/ | ||
| data/ | ||
| results/ | ||
| .DS_Store | ||
| testing/ | ||
| testing* | ||
| *.pyc | ||
| bin/ | ||
| modules/nf-core/ | ||
| subworkflows/nf-core/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,110 +1,53 @@ | ||
| <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/sarek: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing" /> | ||
| <title>nf-core/sarek 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" /> | ||
| <meta name="description" content="nf-core/sarek: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"> | ||
| <title>nf-core/sarek Pipeline Report</title> | ||
| </head> | ||
| <body> | ||
| <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;"> | ||
|
|
||
| <h1>nf-core/sarek ${version}</h1> | ||
| <h2>Run Name: $runName</h2> | ||
| <img src="cid:nfcorepipelinelogo"> | ||
|
|
||
| <% 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/sarek execution completed unsuccessfully!</h4> | ||
| <h1>nf-core/sarek ${version}</h1> | ||
| <h2>Run Name: $runName</h2> | ||
|
|
||
| <% if (!success){ | ||
| out << """ | ||
| <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;"> | ||
| <h4 style="margin-top:0; color: inherit;">nf-core/sarek execution completed unsuccessfully!</h4> | ||
| <p>The exit status of the task that caused the workflow execution to fail was: <code>$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/sarek 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/sarek</p> | ||
| <p><a href="https://github.com/nf-core/sarek">https://github.com/nf-core/sarek</a></p> | ||
| </div> | ||
| </body> | ||
| <p>nf-core/sarek</p> | ||
| <p><a href="https://github.com/nf-core/sarek">https://github.com/nf-core/sarek</a></p> | ||
|
|
||
| </div> | ||
|
|
||
| </body> | ||
| </html> |
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