Use docker image for wilms-14 CI

.github/workflows/run_cell-type-wilms-tumor-14.yml

@@ -33,41 +33,22 @@ jobs:
   run-module:
     if: github.repository_owner == 'AlexsLemonade'
     runs-on: ubuntu-latest
+    container: public.ecr.aws/openscpca/cell-type-wilms-tumor-14: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: Install system dependencies
+      - name: Install git
         run: |
-          sudo apt-get install -y \
-            jags \
-            libcurl4-openssl-dev \
-            libfribidi-dev \
-            libglpk40 \
-            libharfbuzz-dev \
-            libhdf5-dev \
-            libmagick++-dev \
-            libtiff5-dev
+          apt-get update
+          apt-get install -y git
 
-      - name: Set up renv
-        uses: r-lib/actions/setup-renv@v2
-        with:
-          working-directory: ${{ env.MODULE_PATH }}
-
-      - name: Initialize zellkonverter environment
+      - name: Install aws-cli
         run: |
-          cd ${MODULE_PATH}
-          Rscript -e "proc <- basilisk::basiliskStart(env = zellkonverter::zellkonverterAnnDataEnv(), testload = 'anndata'); basilisk::basiliskStop(proc)"
+          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
 
       # Update this step as needed to download the desired data
       - name: Download test data and results

analyses/cell-type-wilms-tumor-14/run_cell-type-wilms-14.sh

@@ -23,6 +23,8 @@ scratch_dir="scratch"
 results_dir="results"
 data_dir="../../data/current/SCPCP000014"
 
+ls -l ${data_dir}
+
 meta_path="${data_dir}/single_cell_metadata.tsv"
 
 
@@ -31,22 +33,26 @@ meta_path="${data_dir}/single_cell_metadata.tsv"
 step_name="00_preprocess_reference"
 scratch_dir_step="${scratch_dir}/${step_name}" && mkdir -p ${scratch_dir_step}
 
+
+
 # Download and process reference data
 ref_h5ad="${scratch_dir_step}/Fetal_full_v3.h5ad"
 ref_seurat="${scratch_dir_step}/kidneyatlas.rdsSeurat"
 ref_seurat_sct="${scratch_dir_step}/kidneyatlas_SCT.rdsSeurat"
 
+echo "Downloading reference data"
 if [[ ! -e ${ref_h5ad} ]]; then
     ref_url="https://cellgeni.cog.sanger.ac.uk/kidneycellatlas/Fetal_full_v3.h5ad"
     curl -s -o ${ref_h5ad} ${ref_url}
 fi
 
+echo "Processing reference data"
 Rscript scripts/${step_name}.R \
     --in_fetal_atlas "${ref_h5ad}" \
     --out_fetal_atlas "${ref_seurat}" \
     $SCT_FLAG
 
-
+echo "Preprocessing data"
 ## Preprocess data
 Rscript scripts/00_preprocessing_rds.R
 
@@ -59,6 +65,7 @@ Rscript scripts/00_preprocessing_rds.R
 #   --libraries SCPCL000846,SCPCL000847  \
 #    $TEST_FLAG
 
+echo "running anchor transfer"
 # run all samples
 Rscript scripts/01_anchor_transfer_seurat.R \
   --reference "${ref_seurat}" \
@@ -67,6 +74,7 @@ Rscript scripts/01_anchor_transfer_seurat.R \
   $SCT_FLAG \
   $TEST_FLAG
 
+echo "summarizing results"
 Rscript scripts/summary_results.R \
   --metadata "${meta_path}" \
   $TEST_FLAG