final setup and run

.github/workflows/ingestion-ci.yml

@@ -67,7 +67,21 @@ jobs:
         run: curl -o pipeline.yml https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/9a4fcbc3c0a4fdc8e6578d086a88730f/pipeline.yml
 
       - name: Preparing the submission file
-        run: curl -o sample_file_qc.txt https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/40ed291bf9a7ff73c4f396ec63cff2f7/sample_file_qc.txt        
+        run: curl -o sample_file_qc.txt https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/40ed291bf9a7ff73c4f396ec63cff2f7/sample_file_qc.txt
+
+      - name: Preparing the QC gene lists
+        run: curl -o qc_genelist_1.0.csv https://panpipes-tutorials.readthedocs.io/en/latest/_downloads/fd38f25644105ea357a26e78a59139bb/qc_genelist_1.0.csv
+
+      - name: Replace template contents in configuration file
+        run: sed 's+panpipes-tutorials/tutorials/ingesting_data/qc_genelist_1.0.csv+qc_genelist_1.0.csv+g' pipeline.yml
+
+      - name: Review pipeline tasks
+        shell: bash -el {0}
+        run: panpipes ingest show full --local
+
+      - name: Run pipeline tasks
+        shell: bash -el {0}
+        run: panpipes ingest make full --local
 
       - name: File tree
         if: env.debug == 'true'