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Quarto GHA Workflow Runner committed Mar 16, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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45 changes: 34 additions & 11 deletions packages.html
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<h2 id="toc-title">On this page</h2>

<ul>
<li><a href="#wilds-packages" id="toc-wilds-packages" class="nav-link active" data-scroll-target="#wilds-packages">WILDS Packages</a></li>
<li><a href="#wilds-packages" id="toc-wilds-packages" class="nav-link active" data-scroll-target="#wilds-packages">WILDS Packages</a>
<ul class="collapse">
<li><a href="#r-packages" id="toc-r-packages" class="nav-link" data-scroll-target="#r-packages">R packages</a></li>
<li><a href="#python-packages" id="toc-python-packages" class="nav-link" data-scroll-target="#python-packages">Python packages</a></li>
<li><a href="#docker" id="toc-docker" class="nav-link" data-scroll-target="#docker">Docker</a></li>
<li><a href="#research-compendia" id="toc-research-compendia" class="nav-link" data-scroll-target="#research-compendia">Research Compendia</a></li>
<li><a href="#wdls" id="toc-wdls" class="nav-link" data-scroll-target="#wdls">WDL’s</a></li>
<li><a href="#nextflow" id="toc-nextflow" class="nav-link" data-scroll-target="#nextflow">NextFlow</a></li>
</ul></li>
</ul>
</nav>
</div>
Expand Down Expand Up @@ -158,24 +166,39 @@ <h1 class="title">Packages</h1>

<section id="wilds-packages" class="level2">
<h2 class="anchored" data-anchor-id="wilds-packages">WILDS Packages</h2>
<section id="r-packages" class="level3">
<h3 class="anchored" data-anchor-id="r-packages">R packages</h3>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/rcromwell" target="_blank">rcromwell</a> - R client for interacting with Cromwell with WDL workflows</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-wdl-SRA-STAR" target="_blank">tg-wdl-SRA-STAR</a> - Workflow to download paired fastqs from SRA and pass through STAR 2 pass</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-wdl-cellRanger" target="_blank">tg-wdl-cellRanger</a> - A basic starting point for a cell ranger workflow</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-star-deseq2-wdl" target="_blank">tg-star-deseq2-wdl</a> - A demo repo to help folks run Star on RNA seq data and do DEseq2</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/sixtyfour" target="_blank">sixtyfour</a> - 🚚 CEO, entrepreneur</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/guide" target="_blank">guide</a> - WILDS Dev Guide</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/badges" target="_blank">badges</a> - WILDS Badges</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/makefiles" target="_blank">makefiles</a> - Makefile templates for WILDS projects</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/getwilds.github.io" target="_blank">getwilds.github.io</a> - WILDS Website</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/cancerprof" target="_blank">cancerprof</a> - API Client for State Cancer Profiles</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/proofr" target="_blank">proofr</a> - Client for the PROOF API</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/fastq-to-cram" target="_blank">fastq-to-cram</a> - Self-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/bs" target="_blank">bs</a> - Bootstrap Components for DASL Projects</p>
</section>
<section id="python-packages" class="level3">
<h3 class="anchored" data-anchor-id="python-packages">Python packages</h3>
<p>Coming soon!</p>
</section>
<section id="docker" class="level3">
<h3 class="anchored" data-anchor-id="docker">Docker</h3>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/wilds-docker-library" target="_blank">wilds-docker-library</a> - Central location for all Docker containers associated with WILDS workflows</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/.github" target="_blank">.github</a></p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/wdl-101" target="_blank">wdl-101</a> - This is the repository for the WDL and JSON files accompanying the WDL 101 course.</p>
</section>
<section id="research-compendia" class="level3">
<h3 class="anchored" data-anchor-id="research-compendia">Research Compendia</h3>
<p>Coming soon!</p>
</section>
<section id="wdls" class="level3">
<h3 class="anchored" data-anchor-id="wdls">WDL’s</h3>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-wdl-SRA-STAR" target="_blank">tg-wdl-SRA-STAR</a> - Workflow to download paired fastqs from SRA and pass through STAR 2 pass</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-wdl-cellRanger" target="_blank">tg-wdl-cellRanger</a> - A basic starting point for a cell ranger workflow</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/tg-star-deseq2-wdl" target="_blank">tg-star-deseq2-wdl</a> - A demo repo to help folks run Star on RNA seq data and do DEseq2</p>
<p><i class="fa-solid fa-box-open" aria-label="box-open"></i> <a href="https://github.com/getwilds/fastq-to-cram" target="_blank">fastq-to-cram</a> - Self-contained WDL workflow that converts a WGS FASTQ file into an unmapped CRAM file</p>
</section>
<section id="nextflow" class="level3">
<h3 class="anchored" data-anchor-id="nextflow">NextFlow</h3>
<p>Coming soon!</p>


</section>
</section>

</main> <!-- /main -->
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50 changes: 25 additions & 25 deletions search.json
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Expand All @@ -42,11 +21,25 @@
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Expand All @@ -61,5 +54,12 @@
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22 changes: 11 additions & 11 deletions sitemap.xml
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