Merge pull request #936 from allyhawkins/allyhawkins/ontology-explora…

…tion

Exploration notebook for creating a reference of consensus labels

.github/components/dictionary.txt

@@ -121,6 +121,7 @@ Jitter
 JSON
 Jupyter
 karyotyping
+LCA
 leiden
 LGBTQ
 licensor

.github/workflows/run_all-modules.yml

@@ -40,6 +40,9 @@ jobs:
   cell-type-nonETP-ALL-03:
       uses: ./.github/workflows/run_cell-type-nonETP-ALL-03.yml
 
+  cell-type-consensus:
+      uses: ./.github/workflows/run_cell-type-consensus.yml
+
       ## Add additional modules above this comment, and to the needs list below
   check-jobs:
     if: ${{ always() }}
@@ -52,6 +55,7 @@ jobs:
       - cell-type-wilms-14
       - cell-type-ETP-ALL-03
       - cell-type-nonETP-ALL-03
+      - cell-type-consensus
     runs-on: ubuntu-latest
     steps:
       - name: Checkout template file

.github/workflows/run_cell-type-consensus.yml

@@ -19,39 +19,32 @@ concurrency:
 
 on:
   workflow_dispatch:
-  # workflow_call:
-  # pull_request:
-  #   branches:
-  #     - main
-  #   paths:
-  #     - analyses/cell-type-consensus/**
-  #     - "!analyses/cell-type-consensus/Dockerfile"
-  #     - "!analyses/cell-type-consensus/.dockerignore"
-  #     - .github/workflows/run_cell-type-consensus.yml
+  workflow_call:
+  pull_request:
+    branches:
+      - main
+    paths:
+      - analyses/cell-type-consensus/**
+      - "!analyses/cell-type-consensus/Dockerfile"
+      - "!analyses/cell-type-consensus/.dockerignore"
+      - .github/workflows/run_cell-type-consensus.yml
 
 jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'
     runs-on: ubuntu-latest
+    container: public.ecr.aws/openscpca/cell-type-consensus:latest
 
     steps:
+      - name: Install aws-cli 
+        run: | 
+          curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" 
+          unzip -q awscliv2.zip 
+          ./aws/install 
+
       - 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