Template update for nf-core/tools version 2.4
nf-core-bot
2 years ago
parent
feeb8ba8dd
commit
a560492353
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name: Fix linting from a comment
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on:
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issue_comment:
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types: [created]
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jobs:
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deploy:
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# Only run if comment is on a PR with the main repo, and if it contains the magic keywords
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if: >
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contains(github.event.comment.html_url, '/pull/') &&
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contains(github.event.comment.body, '@nf-core-bot fix linting') &&
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github.repository == 'nf-core/taxprofiler'
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runs-on: ubuntu-latest
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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@v3
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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# Action runs on the issue comment, so we don't get the PR by default
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# Use the gh cli to check out the PR
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- name: Checkout Pull Request
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run: gh pr checkout ${{ github.event.issue.number }}
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env:
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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- uses: actions/setup-node@v2
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- name: Install Prettier
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run: npm install -g prettier @prettier/plugin-php
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# Check that we actually need to fix something
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- name: Run 'prettier --check'
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id: prettier_status
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run: |
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if prettier --check ${GITHUB_WORKSPACE}; then
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echo "::set-output name=result::pass"
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else
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echo "::set-output name=result::fail"
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fi
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- name: Run 'prettier --write'
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if: steps.prettier_status.outputs.result == 'fail'
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run: prettier --write ${GITHUB_WORKSPACE}
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- name: Commit & push changes
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if: steps.prettier_status.outputs.result == 'fail'
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run: |
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git config user.email "core@nf-co.re"
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git config user.name "nf-core-bot"
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git config push.default upstream
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git add .
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git status
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git commit -m "[automated] Fix linting with Prettier"
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git push
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@ -0,0 +1,9 @@
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email_template.html
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.nextflow*
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work/
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data/
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results/
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.DS_Store
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testing/
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testing*
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*.pyc
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@ -1,111 +1,53 @@
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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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<!-- 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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<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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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<img src="cid:nfcorepipelinelogo">
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<% if (!success){ out << """
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<div
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style="
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color: #a94442;
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background-color: #f2dede;
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border-color: #ebccd1;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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<h4 style="margin-top: 0; color: inherit">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<h1>nf-core/taxprofiler v${version}</h1>
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<h2>Run Name: $runName</h2>
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<% if (!success){
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out << """
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<div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
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<h4 style="margin-top:0; color: inherit;">nf-core/taxprofiler execution completed unsuccessfully!</h4>
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<p>The exit status of the task that caused the workflow execution to fail was: <code>$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">${errorReport}</pre>
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</div>
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""" } else { out << """
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<div
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style="
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color: #3c763d;
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background-color: #dff0d8;
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border-color: #d6e9c6;
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padding: 15px;
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margin-bottom: 20px;
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border: 1px solid transparent;
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border-radius: 4px;
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"
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>
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<pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${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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nf-core/taxprofiler execution completed successfully!
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</div>
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""" } %>
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</div>
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"""
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}
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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
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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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$commandLine</pre
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>
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<p>The workflow was completed at <strong>$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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<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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<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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<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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