Module Test Status
==================

This page is generated from the LENS Nextflow sources during the Sphinx build.
Each row corresponds to a unique RAFT module found in the recursive
dependency tree rooted at ``lens/lens.nf``.

The badge and live pipeline lookup both target branch ``main`` in the
corresponding GitLab repository. Override that branch at build time with
``LENS_MODULE_BADGE_REF`` if the module repos move to a different default branch.
The richer status columns are populated client-side from the public GitLab API
when the page loads. The badge remains as a fallback if the API call fails.
For these module repos, pipeline status is effectively test status because CI is
defined as a single ``pytest`` stage.

.. raw:: html

   <table id="module-test-status-table" class="docutils align-default">
     <thead>
       <tr>
         <th>Module</th>
         <th>GitLab</th>
         <th>Live status</th>
         <th>Last updated</th>
         <th>Latest pipeline</th>
         <th>Badge</th>
       </tr>
     </thead>
     <tbody>
    <tr data-project-path="reproducible-analyses-framework-and-tools/alignment" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/alignment"><code>alignment</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/alignment/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/alignment/-/badges/main/pipeline.svg" alt="alignment pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/annotation" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/annotation"><code>annotation</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/annotation/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/annotation/-/badges/main/pipeline.svg" alt="annotation pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/bcftools" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/bcftools"><code>bcftools</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/bcftools/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/bcftools/-/badges/main/pipeline.svg" alt="bcftools pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/fusion" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/fusion"><code>fusion</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/fusion/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/fusion/-/badges/main/pipeline.svg" alt="fusion pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/gene_signatures" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/gene_signatures"><code>gene_signatures</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/gene_signatures/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/gene_signatures/-/badges/main/pipeline.svg" alt="gene_signatures pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/germline" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/germline"><code>germline</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/germline/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/germline/-/badges/main/pipeline.svg" alt="germline pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/htslib" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/htslib"><code>htslib</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/htslib/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/htslib/-/badges/main/pipeline.svg" alt="htslib pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/igv_reports" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/igv_reports"><code>igv_reports</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/igv_reports/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/igv_reports/-/badges/main/pipeline.svg" alt="igv_reports pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/immuno" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/immuno"><code>immuno</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/immuno/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/immuno/-/badges/main/pipeline.svg" alt="immuno pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/lenstools" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/lenstools"><code>lenstools</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/lenstools/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/lenstools/-/badges/main/pipeline.svg" alt="lenstools pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/neos" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/neos"><code>neos</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/neos/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/neos/-/badges/main/pipeline.svg" alt="neos pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/onco" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/onco"><code>onco</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/onco/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/onco/-/badges/main/pipeline.svg" alt="onco pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/preproc" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/preproc"><code>preproc</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/preproc/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/preproc/-/badges/main/pipeline.svg" alt="preproc pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/qc" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/qc"><code>qc</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/qc/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/qc/-/badges/main/pipeline.svg" alt="qc pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/regtools" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/regtools"><code>regtools</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/regtools/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/regtools/-/badges/main/pipeline.svg" alt="regtools pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/rna_quant" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/rna_quant"><code>rna_quant</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/rna_quant/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/rna_quant/-/badges/main/pipeline.svg" alt="rna_quant pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/samtools" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/samtools"><code>samtools</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/samtools/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/samtools/-/badges/main/pipeline.svg" alt="samtools pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/seq_variation" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/seq_variation"><code>seq_variation</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/seq_variation/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/seq_variation/-/badges/main/pipeline.svg" alt="seq_variation pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/seqtk" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/seqtk"><code>seqtk</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/seqtk/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/seqtk/-/badges/main/pipeline.svg" alt="seqtk pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/somatic" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/somatic"><code>somatic</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/somatic/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/somatic/-/badges/main/pipeline.svg" alt="somatic pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/splice" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/splice"><code>splice</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/splice/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/splice/-/badges/main/pipeline.svg" alt="splice pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/subjoin" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/subjoin"><code>subjoin</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/subjoin/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/subjoin/-/badges/main/pipeline.svg" alt="subjoin pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/tximport" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/tximport"><code>tximport</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/tximport/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/tximport/-/badges/main/pipeline.svg" alt="tximport pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/utilities" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/utilities"><code>utilities</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/utilities/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/utilities/-/badges/main/pipeline.svg" alt="utilities pipeline status (main)"></td>
    </tr>
    <tr data-project-path="reproducible-analyses-framework-and-tools/viral" data-badge-ref="main">
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/viral"><code>viral</code></a></td>
      <td><a href="https://gitlab.com/reproducible-analyses-framework-and-tools/viral/-/pipelines?ref=main">pipelines</a></td>
      <td class="module-live-status">Loading...</td>
      <td class="module-live-updated">-</td>
      <td class="module-live-pipeline"><span>-</span></td>
      <td><img src="https://gitlab.com/reproducible-analyses-framework-and-tools/viral/-/badges/main/pipeline.svg" alt="viral pipeline status (main)"></td>
    </tr>
     </tbody>
   </table>