Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/on…

…tology-exploration

.github/workflows/docker_seurat-conversion.yml

@@ -0,0 +1,63 @@
+# This is a workflow to build the docker image for the seurat-conversion module
+#
+# Docker modules are run on pull requests when code for files that affect the Docker image have changed.
+# If other files are used during the Docker build, they should be added to `paths`
+#
+# At module initialization, this workflow is inactive, and needs to be activated manually
+
+name: Build docker image for seurat-conversion
+
+concurrency:
+  # only one run per branch at a time
+  group: "docker_seurat-conversion_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/seurat-conversion/Dockerfile"
+  #     - "analyses/seurat-conversion/.dockerignore"
+  #     - "analyses/seurat-conversion/renv.lock"
+  #     - "analyses/seurat-conversion/conda-lock.yml"
+  # push:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - "analyses/seurat-conversion/Dockerfile"
+  #     - "analyses/seurat-conversion/.dockerignore"
+  #     - "analyses/seurat-conversion/renv.lock"
+  #     - "analyses/seurat-conversion/conda-lock.yml"
+  workflow_dispatch:
+    inputs:
+      push-ecr:
+        description: "Push to AWS ECR"
+        type: boolean
+        required: true
+
+jobs:
+  test-build:
+    name: Test Build Docker Image
+    if: github.event_name == 'pull_request' || (contains(github.event_name, 'workflow_') && !inputs.push-ecr)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build image
+        uses: docker/build-push-action@v5
+        with:
+          context: "{{defaultContext}}:analyses/seurat-conversion"
+          push: false
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+  build-push:
+    name: Build and Push Docker Image
+    if: github.repository_owner == 'AlexsLemonade' && (github.event_name == 'push' || inputs.push-ecr)
+    uses: ./.github/workflows/build-push-docker-module.yml
+    with:
+      module: "seurat-conversion"
+      push-ecr: true

.github/workflows/run_hello-clusters.yml

@@ -19,15 +19,15 @@ concurrency:
 
 on:
   workflow_dispatch:
-  # workflow_call:
-  # pull_request:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - analyses/hello-clusters/**
-  #     - "!analyses/hello-clusters/Dockerfile"
-  #     - "!analyses/hello-clusters/.dockerignore"
-  #     - .github/workflows/run_hello-clusters.yml
+  workflow_call:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - analyses/hello-clusters/**
+      - "!analyses/hello-clusters/Dockerfile"
+      - "!analyses/hello-clusters/.dockerignore"
+      - .github/workflows/run_hello-clusters.yml
 
 jobs:
   run-module:
@@ -47,16 +47,20 @@ jobs:
       - name: Set up pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Install additional system dependencies
+        run: |
+          sudo apt-get install -y libcurl4-openssl-dev libglpk40
+
       - name: Set up renv
         uses: r-lib/actions/setup-renv@v2
         with:
           working-directory: ${{ env.MODULE_PATH }}
 
-      # Update this step as needed to download the desired data
       - name: Download test data
-        run: ./download-data.py --test-data --format SCE
+        run: ./download-data.py --test-data --format SCE --samples SCPCS000001
 
       - name: Run analysis module
         run: |
           cd ${MODULE_PATH}
-          # run module script(s) here
+          ./run_hello-clusters.sh
+

.github/workflows/run_seurat-conversion.yml

@@ -0,0 +1,62 @@
+# This is a workflow to run the seurat-conversion module
+#
+# Analysis modules are run based on three triggers:
+# - Manual trigger
+# - On pull requests where code in the module has changed
+# - As a reusable workflow called from a separate workflow which periodically runs all modules
+#
+# At initialization, only the manual trigger is active
+
+name: Run seurat-conversion analysis module
+env:
+  MODULE_PATH: analyses/seurat-conversion
+  AWS_DEFAULT_REGION: us-east-2
+
+concurrency:
+  # only one run per branch at a time
+  group: "run_seurat-conversion_${{ github.ref }}"
+  cancel-in-progress: true
+
+on:
+  workflow_dispatch:
+  # workflow_call:
+  # pull_request:
+  #   branches:
+  #     - main
+  #   paths:
+  #     - analyses/seurat-conversion/**
+  #     - "!analyses/seurat-conversion/Dockerfile"
+  #     - "!analyses/seurat-conversion/.dockerignore"
+  #     - .github/workflows/run_seurat-conversion.yml
+
+jobs:
+  run-module:
+    if: github.repository_owner == 'AlexsLemonade'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 4.4.0
+          use-public-rspm: true
+
+      - name: Set up pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Set up renv
+        uses: r-lib/actions/setup-renv@v2
+        with:
+          working-directory: ${{ env.MODULE_PATH }}
+
+      # Update this step as needed to download the desired data
+      - name: Download test data
+        run: ./download-data.py --test-data --format SCE
+
+      - name: Run analysis module
+        run: |
+          cd ${MODULE_PATH}
+          # run module script(s) here

CHANGELOG.md

@@ -17,7 +17,7 @@ The repository at this stage should be generally complete with respect to infras
 
 With respect to infrastructure, the repository contains the following components:
 
-- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io/)
+- detailed documentation in the `docs` directory explaining how to interact with the OpenScPCA project and how to set up and run analyses (published at https://openscpca.readthedocs.io) 
 - a `create-analysis-module.py` script for setting up new analysis modules
 - `download-data.py` and `download-results.py` scripts to download data and results from the OpenScPCA project
 - template notebooks, scripts, environment files, and Docker images for analysis modules

CONTRIBUTING.md

@@ -1,10 +1,10 @@
 # Contributing to OpenScPCA
 
-Please see the [OpenScPCA website](https://openscpca.readthedocs.io/) for information about how to contribute to this project, including:
+Please see the [OpenScPCA website](https://openscpca.readthedocs.io/en/latest) for information about how to contribute to this project, including:
 
 
-* [Obtaining access to data as a formal OpenScPCA contributor](https://openscpca.readthedocs.io/#become-a-contributor)
-* [Setting up](https://openscpca.readthedocs.io/technical-setup)
-* [Contributing to analyses](https://openscpca.readthedocs.io/contributing-to-analyses)
+* [Obtaining access to data as a formal OpenScPCA contributor](https://openscpca.readthedocs.io/en/latest/#become-a-contributor)
+* [Setting up](https://openscpca.readthedocs.io/en/latest/technical-setup)
+* [Contributing to analyses](https://openscpca.readthedocs.io/en/latest/contributing-to-analyses)
 
-Please also review our [Policies](https://openscpca.readthedocs.io/policies) before contributing.
+Please also review our [Policies](https://openscpca.readthedocs.io/en/latest/policies) before contributing.

README.md

@@ -50,7 +50,7 @@ We have comprehensive documentation to help you with various aspects of particip
 
 Please refer to it as you work on the project.
 
-|[OpenScPCA Documentation](https://openscpca.readthedocs.io/)|
+|[OpenScPCA Documentation](https://openscpca.readthedocs.io/en/latest/)|
 |---|
 
 ## Setting up and running analyses

analyses/cell-type-consensus/references/README.md

@@ -16,3 +16,17 @@ To generate this file follow these steps:
 - Download the original reference file with `00-download-panglao-ref.sh`. 
 - Programmatically assign ontology lables with `01-prepare-cell-type-ontologies.sh`. 
 - Assign any ontology values manually by finding the most representive [cell type ontology (CL) identifier term](https://www.ebi.ac.uk/ols4/ontologies/cl). 
+
+There were a few terms that were assigned manually that did not have an obvious or exact match in the cell type ontology that should be noted: 
+
+- `Kidney progenitor cells` were assigned the [`CL:0000324` for metanephric mesenchyme stem cell](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000324). 
+This term refers specifically to the stem cells that ultimately comprise the nephron, but does not account for the part of the kidney that is derived from ureteric bud cells. 
+- `Meningeal cells` were assigned to [`CL:0000708` for leptomeningeal cell](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000708). 
+This was the closest term that covered general cell types found in the meninges. 
+- `Pancreatic progenitor cells` were assigned to [`CL:0002351` for progenitor cell of endocrine pancreas](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0002351). 
+This term only covers progenitor cells for the endocrine pancreas and does not cover the exocrine pancreas. 
+There were no terms that encompassed both other than `progenitor cell`. 
+- `Osteoclast precursor cells` were assigned to [`CL:0000576` for monocyte](https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000576).
+Monocytes differentiate into mononuclear osteoclasts which are then activated and become multinucleated osteoclasts. 
+Because monocytes are the "precursor" to the differentiated osteoclast, we chose to use this term. 
+- `NA` was used for `Undefined placental cells` and `Transient cells` as no clear cell type from the cell ontology was identified.