Merge pull request #127 from haniffalab/dev

Create release 0.5.1

README.md

@@ -14,37 +14,34 @@ The WebAtlas Pipeline uses Nextflow to process spatial and single-cell experimen
 The pipeline can handle data from `h5ad` files, `tif` image files, SpaceRanger, Xenium and MERSCOPE output. It can also generate label 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/webatlas-pipeline/setup.html)
+Full instructions and parameters definitions for this files are available in the [documentation](https://haniffalab.com/webatlas-pipeline/configuration.html)
 
 A parameters file looks like:
 
 ```yaml
 outdir: "/path/to/output/"
 
 args:
-    h5ad:
-        compute_embeddings: "True"
+  h5ad:
+    compute_embeddings: "True"
 
 projects:
   - project: project_1
     datasets:
       - dataset: dataset_1
         data:
-          -
-            data_type: h5ad
+          - data_type: h5ad
             data_path: /path/to/project_1/dataset_1/anndata.h5ad
-          -
-            data_type: raw_image
+          - data_type: raw_image
             data_path: /path/to/project_1/dataset_1/raw_image.tif
-          -
-            data_type: label_image
+          - data_type: label_image
             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"
 ```
 

envs/build-docker-imgs.sh

@@ -1,5 +1,15 @@
 #! /bin/sh
-VERSION=0.5.0
+VERSION=0.5.1
+
+#
+# Build local docker images
+#
+# When using docker the pipleine can use local images or pull them from DockerHub. 
+# If you want to build the images yourself you can do it like this:
+#
+#   cd envs
+#   ./build-docker-imgs.sh
+#
 
 docker build --platform=linux/amd64 -t haniffalab/webatlas-pipeline:${VERSION} -f ./Dockerfile .
 cd build_config/

main.nf

@@ -5,7 +5,7 @@ import groovy.json.*
 nextflow.enable.dsl=2
 
 verbose_log = true
-version = "0.5.0"
+version = "0.5.1"
 
 //////////////////////////////////////////////////////
 

multimodal.nf

@@ -11,7 +11,7 @@ params.outdir = ""
 params.copy_raw = true
 params.description = ""
 
-version="0.5.0"
+version="0.5.1"
 verbose_log=true
 outdir_with_version = "${params.outdir.replaceFirst(/\/*$/, "")}\/${version}"
 

nextflow.config

@@ -13,9 +13,9 @@ profiles {
   docker { 
     docker.enabled = true
     process {
-      container = 'haniffalab/webatlas-pipeline:0.5.0'
+      container = 'haniffalab/webatlas-pipeline:0.5.1'
       withLabel: build_config {
-        container = 'haniffalab/webatlas-pipeline-build-config:0.5.0'
+        container = 'haniffalab/webatlas-pipeline-build-config:0.5.1'
       }
     }
   }

sphinx/citing.rst

@@ -11,4 +11,4 @@ Citation
 
 If you use this software in a scientific publication, please cite using the following Zenodo reference. 
 
-**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.5.0). Zenodo. https://doi.org/10.5281/zenodo.7863308**
+**Li, Tong, Horsfall, David, Basurto-Lozada, Daniela, Prete, Martin, Jessica, Cox, & Iolo, Squires. (2023). WebAtlas Pipeline (v0.5.1). Zenodo. https://doi.org/10.5281/zenodo.7863308**

sphinx/conf.py

@@ -23,7 +23,7 @@
 author = "Haniffa Lab"
 
 # The full version, including alpha/beta/rc tags
-release = "0.5.0"
+release = "0.5.1"
 
 # -- General configuration ---------------------------------------------------
 

sphinx/installation.rst

@@ -14,43 +14,43 @@ Download the WebAtlas Pipeline release. You can look for previous `releases on G
 .. code-block:: shell
    :caption: Input
 
-   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.0.tar.gz
+   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.1.tar.gz
 
 .. code-block:: shell
    :caption: Expected Output
 
    Resolving github.com (github.com)... 140.82.121.3
    Connecting to github.com (github.com)|140.82.121.3|:443... connected.
    HTTP request sent, awaiting response... 302 Found
-   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.0 [following]
-   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.0
+   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.1 [following]
+   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.1
    Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
    Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
    HTTP request sent, awaiting response... 200 OK
    Length: unspecified [application/x-gzip]
-   Saving to: ‘v0.5.0.tar.gz’
+   Saving to: ‘v0.5.1.tar.gz’
 
-   v0.5.0.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
+   v0.5.1.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
 
-   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.0.tar.gz’ saved [2835534]
+   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.1.tar.gz’ saved [2835534]
 
 Extract the WebAtlas compressed tag and change directory into the new repo.
 
 .. code-block:: shell
    :caption: Input
 
-   tar -xzvf ./v0.5.0.tar.gz
-   cd webatlas-pipeline-0.5.0
+   tar -xzvf ./v0.5.1.tar.gz
+   cd webatlas-pipeline-0.5.1
 
 .. code-block:: shell
    :caption: Expected Output
     
-   webatlas-pipeline-0.5.0/
-   webatlas-pipeline-0.5.0/.github/
+   webatlas-pipeline-0.5.1/
+   webatlas-pipeline-0.5.1/.github/
    ...
    ...
-   webatlas-pipeline-0.5.0/tests/input/simple_config.json
-   webatlas-pipeline-0.5.0/tests/test_class.py
+   webatlas-pipeline-0.5.1/tests/input/simple_config.json
+   webatlas-pipeline-0.5.1/tests/test_class.py
 
 .. _environment:
 
@@ -69,7 +69,7 @@ If you have `conda`_ or `mamba`_ already installed then you can use the ``enviro
 .. code-block:: shell
    :caption: Input
 
-   conda env create -f environment.yaml
+   conda env create -f envs/environment.yaml
 
 Then make sure you activate the ``webatlas`` environment beforer you use the pipeline.
 
@@ -78,6 +78,19 @@ Then make sure you activate the ``webatlas`` environment beforer you use the pip
 
    conda activate webatlas
 
+.. warning::
+   Users working on newer Silicon-based Macs may encounter problems installing this environment.
+   Some packages have not yet been compiled for Apple silicon processors therefore, 
+   we recommend you install the packages originally compiled for Mac computers with Intel processors. Set
+   an environment variable that specifies the architecture before installing and activating the Conda
+   environment, like this:
+
+   .. code-block:: shell
+      :caption: Input
+
+      export CONDA_SUBDIR=osx-64
+      conda env create -f envs/environment.yaml 
+      conda activate webatlas
 
 .. _environment_manual:
 
@@ -147,9 +160,9 @@ Enter the following command in your terminal to install nextflow in the current
 
 You can read more about how to install nextflow in the `official nextflow documentation`_.
 
-**#4. Check Docker is installed**
+**#4. Check Docker is installed (optional)**
 
-Make sure Docker Engine 20.10 or later is installed on your computer by using the command:
+If you want to use Docker, make sure Docker Engine 20.10 or later is installed on your computer by using the command:
 
 .. code-block:: shell
    :caption: Input
@@ -169,13 +182,3 @@ Make sure Docker Engine 20.10 or later is installed on your computer by using th
    Context:           default
 
 Follow the `official Docker Install guide`_ if it is not installed already.
-
-**#5. Build local docker images (optional)**
-
-When using docker the pipleine can use local images or pull them from DockerHub. If you want to build the images yourself you can do it like this:
-
-:: 
-
-    cd docker
-    ./build-docker-imgs.sh
-