hotfix: save temporary files (#894)

* save temporary files

* save out

.github/workflows/candig-testing.yml

@@ -67,6 +67,13 @@ jobs:
       - name: Save docker container logs
         if: always()
         run: ./print_logs.sh > tmp/container_logs.txt 2>&1
+      - name: Save any intermediate files in containers
+        if: always()
+        run: |
+              mkdir tmp/ingest
+              docker cp candigv2_candig-ingest_1:/home/candig/tmp tmp/ingest 2>&1
+              mkdir tmp/index
+              docker cp candigv2_htsget_1:/home/candig/tmp tmp/index 2>&1
       - name: Save vault audit logs
         if: always()
         run: docker cp candigv2_vault-runner_1:/vault/vault-audit.log tmp/vault_audit.log 2>&1
@@ -79,3 +86,5 @@ jobs:
                 tmp/progress.txt
                 tmp/container_logs.txt
                 tmp/vault_audit.log
+                tmp/ingest
+                tmp/index