SRP-pipeline tagshttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/tags2020-07-08T09:22:12Zhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/tags/v1.3v1.3v1.3<h1 data-sourcepos="1:1-1:14" dir="auto">
<a id="user-content-new-features" class="anchor" href="#new-features" aria-hidden="true"></a>New features</h1>
<ul data-sourcepos="2:2-5:1" dir="auto">
<li data-sourcepos="2:2-2:246">added new script <code>SCRIPTS/make_ref.py</code> to build references from multiple source (gencode, ensembl, refseq). See wiki page <a href="https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/wikis/usage/reference">Creating a manual reference</a>.</li>
<li data-sourcepos="3:2-3:169">added new statistics in logs created by <code>SCRIPTS/count.py</code> to visualize the number of reads aligned on too many transcripts and reads containing too many mismatches.</li>
<li data-sourcepos="4:2-5:1">added logs in many secondary analysis scripts.</li>
</ul>
<h1 data-sourcepos="6:1-6:9" dir="auto">
<a id="user-content-bug-fix" class="anchor" href="#bug-fix" aria-hidden="true"></a>Bug fix</h1>
<ul data-sourcepos="7:2-9:29" dir="auto">
<li data-sourcepos="7:2-7:78">fixed multiqc reports when analyzing a high number of sample (many plates).</li>
<li data-sourcepos="8:2-8:110">made the new <code>SCRIPTS/make_multiplates_config</code> script backward compatible with ancient configuration files.</li>
<li data-sourcepos="9:2-9:29">fixed bug in README files.</li>
</ul>2020-07-08T09:22:12ZEric Charpentierhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/tags/v1.2v1.2mutliplates<h1 data-sourcepos="1:1-1:14" dir="auto">
<a id="user-content-new-features" class="anchor" href="#new-features" aria-hidden="true"></a>New features</h1>
<ul data-sourcepos="2:2-4:0" dir="auto">
<li data-sourcepos="2:2-2:129">added new snakefile <code>multiplates.smk</code> to run multiplates pipeline. Have a look at <a href="/bird_pipeline_registry/srp-pipeline/-/blob/master/README_multiplates.md" class="gfm">README multiplates</a>.</li>
<li data-sourcepos="3:2-4:0">added the possibility to correct a factor with deseq2 by adding a column in the samplesheet. Procedure described in <a href="/bird_pipeline_registry/srp-pipeline/-/blob/master/README.md" class="gfm">README</a>.</li>
</ul>
<h1 data-sourcepos="5:1-5:9" dir="auto">
<a id="user-content-bug-fix" class="anchor" href="#bug-fix" aria-hidden="true"></a>Bug fix</h1>
<ul data-sourcepos="6:2-6:165" dir="auto">
<li data-sourcepos="6:2-6:165">The absence of annotGo.txt and annotKegg.txt caused the creation of the report to fail. Added check to see if they exist before creating the datatables in report.</li>
</ul>2020-06-24T11:52:27ZEric Charpentierhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/tags/v1.1v1.1Simplified conda environment and report enhancements.<h1 data-sourcepos="1:1-1:30" dir="auto">
<a id="user-content-simplified-conda-environment" class="anchor" href="#simplified-conda-environment" aria-hidden="true"></a>Simplified conda environment</h1>
<ul data-sourcepos="3:1-5:0" dir="auto">
<li data-sourcepos="3:1-3:103">There is now a unique conda environment to install. No more Rscript to install a bunch of R packages.</li>
<li data-sourcepos="4:1-5:0">The installation script has been removed. A simple command to create the conda environment replaces the installation script.</li>
</ul>
<h1 data-sourcepos="6:1-6:21" dir="auto">
<a id="user-content-report-enhancements" class="anchor" href="#report-enhancements" aria-hidden="true"></a>Report enhancements</h1>
<ul data-sourcepos="8:1-9:57" dir="auto">
<li data-sourcepos="8:1-8:101">The volcano and MA-plot have been enhanced. You can now hover on the points to get the genes names.</li>
<li data-sourcepos="9:1-9:57">The enrichment tables have been added for GO and KEGG.</li>
</ul>2020-06-03T14:22:00ZEric Charpentierhttps://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline/-/tags/v1.0v1.0<h2 data-sourcepos="1:1-1:20" dir="auto">
<a id="user-content-first-release-10" class="anchor" href="#first-release-10" aria-hidden="true"></a>First release 1.0</h2>2019-10-14T14:56:33ZEric Charpentier