update webatlas references

Author: dannda

CITATION.cff

@@ -1,8 +1,8 @@
 cff-version: 1.2.0
 type: software
 message: "If you use this repo, please cite it"
-title: "Vitessce Pipeline"
-url: "https://github.com/haniffalab/vitessce-pipeline"
+title: "WebAtlas Pipeline"
+url: "https://github.com/haniffalab/webatlas-pipeline"
 doi: 10.5281/zenodo.7405818
 authors:
   - family-names: "Li"
@@ -11,7 +11,7 @@ authors:
   - family-names: "Horsfall"
     given-names: "Dave"
     orcid: "https://orcid.org/0000-0002-8086-812X"
-  - family-names: "Basurto Lozada"
+  - family-names: "Basurto-Lozada"
     given-names: "Daniela"
     orcid: "https://orcid.org/0000-0003-3943-8424"
   - family-names: "Prete"

README.md

@@ -1,23 +1,23 @@
-[![python-tests](https://github.com/haniffalab/vitessce-pipeline/actions/workflows/tests-python.yml/badge.svg)](https://github.com/haniffalab/vitessce-pipeline/actions/workflows/tests-python.yml)
-[![codecov](https://codecov.io/gh/haniffalab/vitessce-pipeline/branch/main/graph/badge.svg?token=7HQVFH08WJ)](https://codecov.io/gh/haniffalab/vitessce-pipeline/branch/main)
+[![python-tests](https://github.com/haniffalab/webatlas-pipeline/actions/workflows/tests-python.yml/badge.svg)](https://github.com/haniffalab/webatlas-pipeline/actions/workflows/tests-python.yml)
+[![codecov](https://codecov.io/gh/haniffalab/webatlas-pipeline/branch/main/graph/badge.svg?token=7HQVFH08WJ)](https://codecov.io/gh/haniffalab/webatlas-pipeline/branch/main)
 
-# Vitessce Pipeline
+# WebAtlas Pipeline
 
-[![docs](https://img.shields.io/badge/Documentation-online-blue)](https://haniffalab.github.io/vitessce-pipeline)
-[![demo](https://img.shields.io/badge/Demos-view-blue)](https://haniffalab.github.io/vitessce-pipeline/demos.html)
+[![docs](https://img.shields.io/badge/Documentation-online-blue)](https://haniffalab.github.io/webatlas-pipeline)
+[![demo](https://img.shields.io/badge/Demos-view-blue)](https://haniffalab.github.io/webatlas-pipeline/demos.html)
 [![doi](https://zenodo.org/badge/DOI/10.5281/zenodo.7405818.svg)](https://doi.org/10.5281/zenodo.7405818)
 
-This Nextflow pipeline processes spatial and single-cell experiment data for visualisation in [vitessce-app](https://github.com/haniffalab/vitessce-app). The pipeline generates data files for [supported data types](http://vitessce.io/docs/data-types-file-types/), and builds a [view config](http://vitessce.io/docs/view-config-json/).
+This Nextflow pipeline processes spatial and single-cell experiment data for visualisation in [webatlas-app](https://github.com/haniffalab/webatlas-app). The pipeline generates data files for [supported data types](http://vitessce.io/docs/data-types-file-types/), and builds a [view config](http://vitessce.io/docs/view-config-json/).
 
 
 ## Usage
 
 The pipeline can handle data from `h5ad` files, image `tif` files, SpaceRanger output, Xenium output and MERSCOPE output. It can also generate image files from data files.
 
-Running the pipeline requires a `parameters file` that defines configuration options and the data to be processed.
-Full instructions and parameters definitions for this files are available in the [documentation](https://haniffalab.com/vitessce-pipeline/setup.html)
+Running the pipeline requires a parameters file that defines configuration options and the data to be processed.
+Full instructions and parameters definitions for this files are available in the [documentation](https://haniffalab.com/webatlas-pipeline/setup.html)
 
-A `parameters file` looks like
+A parameters file looks like
 
 ```yaml
 outdir: "/path/to/output/"
@@ -57,4 +57,4 @@ nextflow run main.nf -params-file /path/to/run-params.yaml -entry Full_pipeline
 ```
 
 
-`Parameters file` templates are available in the `templates` directory.
+Parameters file templates are available in the `templates` directory.

docker/build-docker-imgs.sh

@@ -8,4 +8,4 @@
 
 VERSION=0.0.1
 
-docker build --platform=linux/amd64 -t haniffalab/vitessce-pipeline:${VERSION} -f ./Dockerfile .
+docker build --platform=linux/amd64 -t haniffalab/webatlas-pipeline:${VERSION} -f ./Dockerfile .

nextflow.config

@@ -2,7 +2,7 @@ singularity.enabled = false
 singularity.autoMounts = false
 
 docker.enabled = true
-process.container = 'haniffalab/vitessce-pipeline:0.0.1'
+process.container = 'haniffalab/webatlas-pipeline:0.0.1'
 
 // see https://www.nextflow.io/docs/latest/config.html#scope-aws
 aws {

sphinx/citing.rst

@@ -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,

sphinx/conf.py

@@ -18,7 +18,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "vitessce-pipeline"
+project = "webatlas-pipeline"
 copyright = "2022, Haniffa Lab"
 author = "Haniffa Lab"
 

sphinx/demos.rst

@@ -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>`__

sphinx/index.rst

@@ -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

sphinx/installation.rst

@@ -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`

sphinx/run.rst

@@ -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.