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diff --git a/docs/build/doctrees/contents.doctree b/docs/build/doctrees/contents.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/further-information/about.doctree b/docs/build/doctrees/further-information/about.doctree
diff --git a/docs/build/doctrees/further-information/example-files.doctree b/docs/build/doctrees/further-information/example-files.doctree
diff --git a/docs/build/doctrees/further-information/faq.doctree b/docs/build/doctrees/further-information/faq.doctree
diff --git a/docs/build/doctrees/further-information/uninstall-dicast.doctree b/docs/build/doctrees/further-information/uninstall-dicast.doctree
diff --git a/docs/build/doctrees/get-started/config.doctree b/docs/build/doctrees/get-started/config.doctree
diff --git a/docs/build/doctrees/get-started/config/ASimulatoR_parameters.doctree b/docs/build/doctrees/get-started/config/ASimulatoR_parameters.doctree
diff --git a/docs/build/doctrees/get-started/config/as_parameters.doctree b/docs/build/doctrees/get-started/config/as_parameters.doctree
diff --git a/docs/build/doctrees/get-started/config/general_parameters.doctree b/docs/build/doctrees/get-started/config/general_parameters.doctree
diff --git a/docs/build/doctrees/get-started/config/snakemake_parameters.doctree b/docs/build/doctrees/get-started/config/snakemake_parameters.doctree
diff --git a/docs/build/doctrees/get-started/run.doctree b/docs/build/doctrees/get-started/run.doctree
diff --git a/docs/build/doctrees/get-started/run/dicast-cli.doctree b/docs/build/doctrees/get-started/run/dicast-cli.doctree
diff --git a/docs/build/doctrees/get-started/run/gui.doctree b/docs/build/doctrees/get-started/run/gui.doctree
diff --git a/docs/build/doctrees/get-started/run/one_tool.doctree b/docs/build/doctrees/get-started/run/one_tool.doctree
diff --git a/docs/build/doctrees/get-started/run/outputs.doctree b/docs/build/doctrees/get-started/run/outputs.doctree
diff --git a/docs/build/doctrees/get-started/setup.doctree b/docs/build/doctrees/get-started/setup.doctree
diff --git a/docs/build/doctrees/get-started/setup/docker.doctree b/docs/build/doctrees/get-started/setup/docker.doctree
diff --git a/docs/build/doctrees/get-started/setup/git.doctree b/docs/build/doctrees/get-started/setup/git.doctree
diff --git a/docs/build/doctrees/get-started/setup/input.doctree b/docs/build/doctrees/get-started/setup/input.doctree
diff --git a/docs/build/doctrees/get-started/setup/snakemake.doctree b/docs/build/doctrees/get-started/setup/snakemake.doctree
diff --git a/docs/build/doctrees/tools/mapping.doctree b/docs/build/doctrees/tools/mapping.doctree
diff --git a/docs/build/doctrees/tools/mapping/bbmap.doctree b/docs/build/doctrees/tools/mapping/bbmap.doctree
diff --git a/docs/build/doctrees/tools/mapping/contextmap.doctree b/docs/build/doctrees/tools/mapping/contextmap.doctree
diff --git a/docs/build/doctrees/tools/mapping/crac.doctree b/docs/build/doctrees/tools/mapping/crac.doctree
diff --git a/docs/build/doctrees/tools/mapping/dart.doctree b/docs/build/doctrees/tools/mapping/dart.doctree
diff --git a/docs/build/doctrees/tools/mapping/gsnap.doctree b/docs/build/doctrees/tools/mapping/gsnap.doctree
diff --git a/docs/build/doctrees/tools/mapping/hisat.doctree b/docs/build/doctrees/tools/mapping/hisat.doctree
diff --git a/docs/build/doctrees/tools/mapping/mapsplice.doctree b/docs/build/doctrees/tools/mapping/mapsplice.doctree
diff --git a/docs/build/doctrees/tools/mapping/minimap.doctree b/docs/build/doctrees/tools/mapping/minimap.doctree
diff --git a/docs/build/doctrees/tools/mapping/segemehl.doctree b/docs/build/doctrees/tools/mapping/segemehl.doctree
diff --git a/docs/build/doctrees/tools/mapping/star.doctree b/docs/build/doctrees/tools/mapping/star.doctree
diff --git a/docs/build/doctrees/tools/mapping/subjunc.doctree b/docs/build/doctrees/tools/mapping/subjunc.doctree
diff --git a/docs/build/doctrees/tools/splicing.doctree b/docs/build/doctrees/tools/splicing.doctree
diff --git a/docs/build/doctrees/tools/splicing/asgal.doctree b/docs/build/doctrees/tools/splicing/asgal.doctree
diff --git a/docs/build/doctrees/tools/splicing/aspli.doctree b/docs/build/doctrees/tools/splicing/aspli.doctree
diff --git a/docs/build/doctrees/tools/splicing/eventpointer.doctree b/docs/build/doctrees/tools/splicing/eventpointer.doctree
diff --git a/docs/build/doctrees/tools/splicing/irfinder.doctree b/docs/build/doctrees/tools/splicing/irfinder.doctree
diff --git a/docs/build/doctrees/tools/splicing/kissplice.doctree b/docs/build/doctrees/tools/splicing/kissplice.doctree
diff --git a/docs/build/doctrees/tools/splicing/majiq.doctree b/docs/build/doctrees/tools/splicing/majiq.doctree
diff --git a/docs/build/doctrees/tools/splicing/sgseq.doctree b/docs/build/doctrees/tools/splicing/sgseq.doctree
diff --git a/docs/build/doctrees/tools/splicing/spladder.doctree b/docs/build/doctrees/tools/splicing/spladder.doctree
diff --git a/docs/build/doctrees/tools/splicing/whippet.doctree b/docs/build/doctrees/tools/splicing/whippet.doctree
diff --git a/docs/build/doctrees/tools/tools.doctree b/docs/build/doctrees/tools/tools.doctree
diff --git a/docs/build/html/_images/upset_plot.png b/docs/build/html/_images/upset_plot.png
diff --git a/docs/build/html/_sources/contents.rst.txt b/docs/build/html/_sources/contents.rst.txt
@@ -11,7 +11,7 @@ To provide a fair baseline while maintaining easy usability, per default we run
 The tools included here are the most widely used and well maintained among AS event detection tools. If you would like to include your tool in the pipeline please let us know.
 We hope this collection can be a starting point for future benchmarking approaches and quality control.
 
-.. figure:: /img/Screenshot_dicast.png
+.. figure:: /img/pipeline.png
 
 
 What is DICAST?

diff --git a/docs/build/html/_sources/get-started/run.rst.txt b/docs/build/html/_sources/get-started/run.rst.txt
@@ -8,9 +8,9 @@ Run your analysis
 .. toctree::
    :maxdepth: 2
 
-   run/gui
    run/dicast-cli
    run/one_tool
+   run/gui
    run/outputs
 
 

diff --git a/docs/build/html/_sources/get-started/run/dicast-cli.rst.txt b/docs/build/html/_sources/get-started/run/dicast-cli.rst.txt
@@ -1,5 +1,5 @@
-Run DICAST via Command Line Interface (depreciated)
-===================================================
+Run DICAST via Command Line Interface 
+======================================
 
 In this section we will explain how to use DICAST to run a whole pipeline on the terminal alone.
 

diff --git a/docs/build/html/_sources/get-started/run/gui.rst.txt b/docs/build/html/_sources/get-started/run/gui.rst.txt
@@ -1,5 +1,5 @@
-Run DICAST with a graphical user interface
-================================================
+Run DICAST with a graphical user interface (depreciated)
+========================================================
 
 .. toctree::
    :maxdepth: 1

diff --git a/docs/build/html/_sources/get-started/run/one_tool.rst.txt b/docs/build/html/_sources/get-started/run/one_tool.rst.txt
@@ -16,7 +16,7 @@ If you have already built the image with <tool>:<tag> (see the :doc:`docker setu
   # If you are using our directory structure for your input and are in the dockers directory:
   # Add the --rm flag to remove container, after run.
 
-  docker run -v ./:/MOUNT --user $(id -u):$(id -g) --rm gsnap:0.1
+  docker run -v $(pwd):/MOUNT --user $(id -u):$(id -g) --rm gsnap:0.1
 
 
 Troubleshooting

diff --git a/docs/build/html/_sources/get-started/setup/docker.rst.txt b/docs/build/html/_sources/get-started/setup/docker.rst.txt
@@ -64,9 +64,18 @@ We support Docker version 19 and above.
 
   docker-compose --version
 
+2. Pull docker images (Not needed with snakemake)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Should the tool you intended to run, not build locally, it's also possible to pull them from DICAST's dockerhub repository at: https://hub.docker.com/repository/docker/dicastproj/dicast
 
 
-2. Build docker images (Optional)
+.. prompt:: bash $
+
+  docker pull dicastproj/dicast:tagname
+
+
+3. Build docker images (For Developers)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 While the steps described in this section are handled by DICAST's graphical interface, it can also be accessed via command line, for more control.
 
@@ -101,17 +110,6 @@ Where <tool> needs to be replaced with one or more of the following tools:
 
 bbmap, contextmap, crac, dart, gsnap, hisat, mapsplice, minimap, segemehl, star, subjunc, asgal, aspli, eventpointer, irfinder, majiq, sgseq, spladder, whippet
 
-
-3. Pull docker images (Fail safe)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Should the tool you intended to run, not build locally, it's also possible to pull them from DICAST's dockerhub repository at: https://hub.docker.com/repository/docker/dicastproj/dicast
-
-
-.. prompt:: bash $
-
-  docker pull dicastproj/dicast:tagname
-
 4. Other helpful commands
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 To gracefully stop a running docker container (If perhaps snakemake's process had to be killed):

diff --git a/docs/build/html/_static/css/badge_only.css b/docs/build/html/_static/css/badge_only.css
diff --git a/docs/build/html/_static/css/theme.css b/docs/build/html/_static/css/theme.css
diff --git a/docs/build/html/contents.html b/docs/build/html/contents.html
@@ -67,13 +67,13 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="get-started/run.html">Run your analysis</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -134,8 +134,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="#" class="icon icon-home"></a> &raquo;</li>
-      <li>Welcome to DICAST!</li>
+      <li><a href="#" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Welcome to DICAST!</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/contents.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -153,7 +153,7 @@ <h1>Welcome to DICAST!<a class="headerlink" href="#welcome-to-dicast" title="Per
 <p>The tools included here are the most widely used and well maintained among AS event detection tools. If you would like to include your tool in the pipeline please let us know.
 We hope this collection can be a starting point for future benchmarking approaches and quality control.</p>
 <figure class="align-default">
-<img alt="_images/Screenshot_dicast.png" src="_images/Screenshot_dicast.png" />
+<img alt="_images/pipeline.png" src="_images/pipeline.png" />
 </figure>
 </section>
 <section id="what-is-dicast">

diff --git a/docs/build/html/further-information/about.html b/docs/build/html/further-information/about.html
@@ -67,13 +67,13 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -134,8 +134,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
-      <li>About</li>
+      <li><a href="../contents.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">About</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/further-information/about.rst.txt" rel="nofollow"> View page source</a>
       </li>

diff --git a/docs/build/html/further-information/example-files.html b/docs/build/html/further-information/example-files.html
@@ -68,13 +68,13 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -135,8 +135,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Examples</li>
+      <li><a href="../contents.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Examples</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/further-information/example-files.rst.txt" rel="nofollow"> View page source</a>
       </li>

diff --git a/docs/build/html/further-information/faq.html b/docs/build/html/further-information/faq.html
@@ -68,13 +68,13 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -135,8 +135,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
-      <li>FAQ</li>
+      <li><a href="../contents.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">FAQ</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/further-information/faq.rst.txt" rel="nofollow"> View page source</a>
       </li>

diff --git a/docs/build/html/further-information/uninstall-dicast.html b/docs/build/html/further-information/uninstall-dicast.html
@@ -68,13 +68,13 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="../get-started/run.html">Run your analysis</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/dicast-cli.html">Run DICAST via Command Line Interface (depreciated)</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="../get-started/run/one_tool.html">Run one specific tool via Docker</a><ul class="simple">
+<li class="toctree-l2"><a class="reference internal" href="../get-started/run/gui.html">Run DICAST with a graphical user interface (depreciated)</a><ul class="simple">
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="../get-started/run/outputs.html">DICAST Outputs</a></li>
@@ -135,8 +135,8 @@
         <div class="rst-content">
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
-      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
-      <li>Uninstalling DICAST</li>
+      <li><a href="../contents.html" class="icon icon-home"></a></li>
+      <li class="breadcrumb-item active">Uninstalling DICAST</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/further-information/uninstall-dicast.rst.txt" rel="nofollow"> View page source</a>
       </li>