Deploying to dev from @ 298edd1 🚀

Author: dannda

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c71381c26124df42bb192e0d691919ed
+config: 3bc1e2994b381fa607cbb5156f366ba3
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_sources/citing.rst.txt

@@ -15,7 +15,7 @@ Cite as
 
 .. raw:: html
 
-   <p><b><i>Li, Tong, Horsfall, Dave, & Basurto Lozada, Daniela. (2022). A nextflow pipeline to process spatial and single-cell data for Vitessce (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.7405819</i></b></p>
+   <p><b><i>Li, Tong, Horsfall, Dave, & Basurto-Lozada, Daniela. (2022). A nextflow pipeline to process spatial and single-cell data for Vitessce (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.7405819</i></b></p>
 
 Bibtex
 ------
@@ -25,7 +25,7 @@ Bibtex
    @software{li_tong_2022_7405819,
       author       = {Li, Tong and
                         Horsfall, Dave and
-                        Basurto Lozada, Daniela},
+                        Basurto-Lozada, Daniela},
       title        = {{A nextflow pipeline to process spatial and single- 
                         cell data for Vitessce}},
       month        = dec,

docs/_sources/demos.rst.txt

@@ -9,19 +9,19 @@ Human Hindlimb
 -  Visium:
 
    -  `Sample
-      1 <https://vitessce-app.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_1_Visium_1_config.json>`__
+      1 <https://webatlas.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_1_Visium_1_config.json>`__
    -  `Sample
-      2 <https://vitessce-app.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_2_Visium_2_config.json>`__
+      2 <https://webatlas.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_2_Visium_2_config.json>`__
    -  `Sample
-      3 <https://vitessce-app.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_3_Visium_3_config.json>`__
+      3 <https://webatlas.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_3_Visium_3_config.json>`__
 
--  `ISS <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?config=https://bayraktar.cog.sanger.ac.uk/iss/0.0.1/ISS_hindlimb_1_config.json>`__
--  `scRNAseq <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/hindlimb/scRNAseq/0.0.1/Hindlimb_scRNAseq_1_config.json>`__
+-  `ISS <https://webatlas.cog.sanger.ac.uk/dev/index.html?config=https://bayraktar.cog.sanger.ac.uk/iss/0.0.1/ISS_hindlimb_1_config.json>`__
+-  `scRNAseq <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/hindlimb/scRNAseq/0.0.1/Hindlimb_scRNAseq_1_config.json>`__
 
 Human Whole Embryo
 ~~~~~~~~~~~~~~~~~~
 
--  `Visium <https://vitessce-app.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_4_config.json>`__
+-  `Visium <https://webatlas.cog.sanger.ac.uk/latest/index.html?config=https://hindlimb.cog.sanger.ac.uk/datasets/Visium/0.0.1/Hindlimb_visium_4_config.json>`__
 
 Fetal Immune
 ~~~~~~~~~~~~
@@ -31,40 +31,40 @@ Fetal Immune
    -  Fetal liver:
 
       -  `Sample
-         1 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_1_config.json>`__
+         1 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_1_config.json>`__
       -  `Sample
-         2 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_2_config.json>`__
+         2 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_2_config.json>`__
       -  `Sample
-         3 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_3_config.json>`__
+         3 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-liver/visium/0.0.1/visium_3_config.json>`__
 
    -  Fetal spleen:
 
       -  `Sample
-         1 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_1_config.json>`__
+         1 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_1_config.json>`__
       -  `Sample
-         2 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_2_config.json>`__
+         2 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_2_config.json>`__
       -  `Sample
-         3 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_3_config.json>`__
+         3 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_3_config.json>`__
       -  `Sample
-         4 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_4_config.json>`__
+         4 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-spleen/visium/0.0.1/visium_4_config.json>`__
 
    -  Fetal thymus:
 
       -  `Sample
-         1 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_1_config.json>`__
+         1 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_1_config.json>`__
       -  `Sample
-         2 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_2_config.json>`__
+         2 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_2_config.json>`__
       -  `Sample
-         3 <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_3_config.json>`__
+         3 <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/fetal-thymus/visium/0.0.1/visium_3_config.json>`__
 
--  `scRNAseq <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/scrnaseq/umap.json>`__
+-  `scRNAseq <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/fetal-immune/scrnaseq/umap.json>`__
 
 Breast Cancer
 ~~~~~~~~~~~~~
 
--  `Xenium <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/breast-cancer/xenium/config.json>`__
+-  `Xenium <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/breast-cancer/xenium/config.json>`__
 
 Yolk sac
 ~~~~~~~~
 
--  `RNAScope <https://vitessce-app.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/yolk-sac/rnascope/hiplex.json>`__
+-  `RNAScope <https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=https://haniffa.cog.sanger.ac.uk/yolk-sac/rnascope/hiplex.json>`__

docs/_sources/index.rst.txt

@@ -1,21 +1,21 @@
 |Tests| |Sphinx| |Coverage| |DOI|
 
-.. |Tests| image:: https://github.com/haniffalab/vitessce-pipeline/actions/workflows/tests-python.yml/badge.svg
-   :target: https://github.com/haniffalab/vitessce-pipeline/actions/workflows/tests-python.yml
-.. |Sphinx| image:: https://github.com/haniffalab/vitessce-pipeline/actions/workflows/sphinx-build.yml/badge.svg
-   :target: https://github.com/haniffalab/vitessce-pipeline/actions/workflows/sphinx-build.yml
-.. |Coverage| image:: https://codecov.io/gh/haniffalab/vitessce-pipeline/branch/main/graph/badge.svg?token=7HQVFH08WJ
-   :target: https://codecov.io/gh/haniffalab/vitessce-pipeline/branch/main
+.. |Tests| image:: https://github.com/haniffalab/webatlas-pipeline/actions/workflows/tests-python.yml/badge.svg
+   :target: https://github.com/haniffalab/webatlas-pipeline/actions/workflows/tests-python.yml
+.. |Sphinx| image:: https://github.com/haniffalab/webatlas-pipeline/actions/workflows/sphinx-build.yml/badge.svg
+   :target: https://github.com/haniffalab/webatlas-pipeline/actions/workflows/sphinx-build.yml
+.. |Coverage| image:: https://codecov.io/gh/haniffalab/webatlas-pipeline/branch/main/graph/badge.svg?token=7HQVFH08WJ
+   :target: https://codecov.io/gh/haniffalab/webatlas-pipeline/branch/main
 .. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.7405818.svg
    :target: https://doi.org/10.5281/zenodo.7405818
 
-Vitessce Pipeline
+WebAtlas Pipeline
 =================
 
-This Nextflow pipeline processes spatial and single-cell experiment data for visualisation in `Vitessce`_. 
+This Nextflow pipeline processes spatial and single-cell experiment data for visualisation in `WebAtlas App`_. 
 The pipeline generates data files for `supported data types`_, and builds a `view config`_.
 
-.. _Vitessce: https://github.com/haniffalab/vitessce-app
+.. _WebAtlas App: https://github.com/haniffalab/webatlas-app
 .. _supported data types: https://vitessce.io/docs/data-types-file-types/
 .. _view config: https://vitessce.io/docs/view-config-json/
 
@@ -43,9 +43,9 @@ Indices and tables
 
    demos
    citing
-   Source Code <https://github.com/haniffalab/vitessce-pipeline>
-   Issue Tracker <https://github.com/haniffalab/vitessce-pipeline/issues>
-   Frontend Client <https://github.com/haniffalab/vitessce-app>
+   Source Code <https://github.com/haniffalab/webatlas-pipeline>
+   Issue Tracker <https://github.com/haniffalab/webatlas-pipeline/issues>
+   Frontend Client <https://github.com/haniffalab/webatlas-app>
 
 .. toctree::
    :maxdepth: 2

docs/_sources/installation.rst.txt

@@ -7,8 +7,8 @@ Installation
 
 ::
     
-    git clone git@github.com:haniffalab/vitessce-pipeline.git
-    cd vitessce-pipeline
+    git clone git@github.com:haniffalab/webatlas-pipeline.git
+    cd webatlas-pipeline
     
 2. Install nextflow by following the `documentation`_
 3. Install `Docker`_ and make sure it's in :code:`PATH`

docs/_sources/run.rst.txt

@@ -34,7 +34,7 @@ Use ``-entry Process_files`` or ``-entry Process_images`` as you need.
 Further reading:
 ----------------
 
-Docker image pulling/local conda env creation are handled by nextflow.
+Docker image pulling/local conda env creation are handled by Nextflow.
 Please refer to
 `this <https://www.nextflow.io/docs/latest/getstarted.html>`__ for
 detailed information.
@@ -43,7 +43,7 @@ detailed information.
 Visualizing
 ===========
 
-Vitessce
+WebAtlas
 --------
 
 The pipeline generates a Vitessce view config file for each processed dataset.
@@ -72,9 +72,9 @@ In this case, using `serve <https://www.npmjs.com/package/serve>`__, this is don
 
 Your view configs should then be accessible at ``http://localhost:3000/{project}-{dataset}-config.json``.
 
-You can then load them in a Vitessce instance like the `Vitessce app <https://github.com/haniffalab/vitessce-app>`__ 
-deployed at `<https://vitessce-app.cog.sanger.ac.uk/latest/index.html>`__.
+You can then load them in a Vitessce instance like the `WebAtlas app <https://github.com/haniffalab/webatlas-app>`__ 
+deployed at `<https://webatlas.cog.sanger.ac.uk/latest/index.html>`__.
 
 Specify your locally served view config through the ``config`` parameter like
-``https://vitessce-app.cog.sanger.ac.uk/latest/index.html?config=http://localhost:3000/{project}-{dataset}-config.json``
+``https://webatlas.cog.sanger.ac.uk/latest/index.html?config=http://localhost:3000/{project}-{dataset}-config.json``
 and load this URL in your browser to visualize your data in a Vitessce viewer.

docs/_sources/setup.rst.txt

@@ -4,7 +4,7 @@
 Setup
 #####
 
-Currently, the pipeline can process several types of data files as well as images.
+Currently, the WebAtlas pipeline can process several types of data files as well as images.
 
 - It can handle ``h5ad`` files, SpaceRanger output, Xenium output, MERSCOPE output, and ``molecules`` data in ``csv``/``tsv`` files.
 - It can handle raw and label images in ``tif`` format, as well as generating/preprocessing images from Visium, Xenium and MERFISH data. 
@@ -31,8 +31,8 @@ A parameters file looks like:
     outdir: "/path/to/output/"
     
     args:
-        h5ad:
-            compute_embeddings: "True"
+      h5ad:
+        compute_embeddings: "True"
     
     projects:
       - project: project_1
@@ -50,10 +50,10 @@ A parameters file looks like:
                 data_path: /path/to/project_1/dataset_1/label_image.tif
 
     vitessce_options:
-        spatial:
-            xy: "obsm/spatial"
-        mappings:
-            obsm/X_umap: [0,1]
+      spatial:
+        xy: "obsm/spatial"
+      mappings:
+        obsm/X_umap: [0,1]
     layout: "simple"
     # custom_layout: "spatial|scatterplot" # overrides `layout`
 

docs/citing.html

@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Citation &mdash; vitessce-pipeline 0.1.0 documentation</title>
+  <title>Citation &mdash; webatlas-pipeline 0.1.0 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -29,7 +29,7 @@
 
 
           <a href="index.html" class="icon icon-home">
-            vitessce-pipeline
+            webatlas-pipeline
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -56,9 +56,9 @@
 <li class="toctree-l2"><a class="reference internal" href="#bibtex">Bibtex</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/vitessce-pipeline">Source Code</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/vitessce-pipeline/issues">Issue Tracker</a></li>
-<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/vitessce-app">Frontend Client</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/webatlas-pipeline">Source Code</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/webatlas-pipeline/issues">Issue Tracker</a></li>
+<li class="toctree-l1"><a class="reference external" href="https://github.com/haniffalab/webatlas-app">Frontend Client</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">Project Teams</span></p>
 <ul>
@@ -73,7 +73,7 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="index.html">vitessce-pipeline</a>
+          <a href="index.html">webatlas-pipeline</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -97,13 +97,13 @@
 <p>If you use this software in a scientific publication, please cite using the following Zenodo reference.</p>
 <section id="cite-as">
 <h2>Cite as<a class="headerlink" href="#cite-as" title="Permalink to this heading"></a></h2>
-<p><b><i>Li, Tong, Horsfall, Dave, & Basurto Lozada, Daniela. (2022). A nextflow pipeline to process spatial and single-cell data for Vitessce (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.7405819</i></b></p></section>
+<p><b><i>Li, Tong, Horsfall, Dave, & Basurto-Lozada, Daniela. (2022). A nextflow pipeline to process spatial and single-cell data for Vitessce (0.1.0). Zenodo. https://doi.org/10.5281/zenodo.7405819</i></b></p></section>
 <section id="bibtex">
 <h2>Bibtex<a class="headerlink" href="#bibtex" title="Permalink to this heading"></a></h2>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@software</span><span class="p">{</span><span class="n">li_tong_2022_7405819</span><span class="p">,</span>
    <span class="n">author</span>       <span class="o">=</span> <span class="p">{</span><span class="n">Li</span><span class="p">,</span> <span class="n">Tong</span> <span class="ow">and</span>
                      <span class="n">Horsfall</span><span class="p">,</span> <span class="n">Dave</span> <span class="ow">and</span>
-                     <span class="n">Basurto</span> <span class="n">Lozada</span><span class="p">,</span> <span class="n">Daniela</span><span class="p">},</span>
+                     <span class="n">Basurto</span><span class="o">-</span><span class="n">Lozada</span><span class="p">,</span> <span class="n">Daniela</span><span class="p">},</span>
    <span class="n">title</span>        <span class="o">=</span> <span class="p">{{</span><span class="n">A</span> <span class="n">nextflow</span> <span class="n">pipeline</span> <span class="n">to</span> <span class="n">process</span> <span class="n">spatial</span> <span class="ow">and</span> <span class="n">single</span><span class="o">-</span>
                      <span class="n">cell</span> <span class="n">data</span> <span class="k">for</span> <span class="n">Vitessce</span><span class="p">}},</span>
    <span class="n">month</span>        <span class="o">=</span> <span class="n">dec</span><span class="p">,</span>