adjust spatial preprocessing to spatialData

.github/workflows/spatial_preprocess-ci.yml

@@ -53,19 +53,62 @@ jobs:
         shell: pwsh
         run: conda list
 
-
       - name: Preparing the data
         run: |
-          mkdir spatial spatial/preprocess spatial/preprocess/data
-          cd spatial/preprocess/data 
-          
-          curl -L -o V1_Human_Heart_unfilt.h5mu https://figshare.com/ndownloader/files/45031048
-          curl -L -o V1_Human_Lymph_Node_unfilt.h5mu https://figshare.com/ndownloader/files/45031051
+          mkdir spatial spatial/ingestion spatial/ingestion/data
+          cd spatial/ingestion/data 
+          mkdir V1_Human_Heart V1_Human_Lymph_Node
+          cd V1_Human_Heart
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_filtered_feature_bc_matrix.h5
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Heart/V1_Human_Heart_spatial.tar.gz
+          tar -xf V1_Human_Heart_spatial.tar.gz
+          cd ../V1_Human_Lymph_Node
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.h5
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/1.0.0/V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz
+          tar -xf V1_Human_Lymph_Node_spatial.tar.gz
 
       # Note: we run the following to test that the commands works
       - name: Preparing the configuration file
         shell: bash -el {0}
         run: |
+          cd spatial/ingestion
+          panpipes qc_spatial config
+
+      - name: Preparing the submission file
+        run: |
+          cd spatial/ingestion
+          curl -o sample_file_qc_visium.txt https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_visium_data/sample_file_qc_visium.txt
+      - name: Preparing the yaml file
+        run: |
+          cd spatial/ingestion
+          curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/sarah_spatialData/docs/ingesting_visium_data/pipeline.yml
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree spatial/ingestion
+
+      - name: Review pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd spatial/ingestion
+          panpipes qc_spatial show full --local
+
+      - name: Run pipeline tasks
+        shell: bash -el {0}
+        run: |
+          cd spatial/ingestion
+          panpipes qc_spatial make full --local
+
+      - name: File tree
+        if: env.debug == 'true'
+        run: tree spatial/ingestion
+
+
+      # Note: we run the following to test that the commands works
+      - name: Preparing the configuration file
+        shell: bash -el {0}
+        run: |
+          mkdir spatial/preprocess 
           cd spatial/preprocess
           panpipes preprocess_spatial config
 
@@ -74,11 +117,6 @@ jobs:
           cd spatial/preprocess
           curl -o pipeline.yml https://raw.githubusercontent.com/DendrouLab/panpipes-tutorials/main/docs/preprocess_spatial_data/pipeline.yml
 
-      - name: Replace template contents in configuration file
-        run: |
-          cd spatial/preprocess
-          sed -i 's+../ingestion/qc.data/+./data/+g' pipeline.yml
-
       - name: File tree
         if: env.debug == 'true'
         run: tree spatial/preprocess