Fixed handling of control_gvcf_dir when not provided; Fixed assignmen…

…t of workflow name
RTIInternational · Oct 30, 2024 · 7123ffd · 7123ffd
1 parent b68be8a
commit 7123ffd
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/t1dgrs2_pipeline/v2.0/Dockerfile b/t1dgrs2_pipeline/v2.0/Dockerfile
@@ -83,4 +83,3 @@ WORKDIR /data
 RUN chown -R docker:staff /data
 
 ENTRYPOINT [ "/opt/entrypoint.sh" ]
-
diff --git a/t1dgrs2_pipeline/v2.0/scripts/batch_extract_gvcf_variants.py b/t1dgrs2_pipeline/v2.0/scripts/batch_extract_gvcf_variants.py
@@ -101,7 +101,7 @@ def get_running_workflows():
 os.system("mkdir -p {}".format(gvcf_dir))
 output_dir = args.output_dir if (args.output_dir[-1] == "/") else (args.output_dir + "/")
 os.system("mkdir -p {}".format(output_dir))
-if args.control_gvcf_dir is None:
+if args.control_gvcf_dir is None or args.control_gvcf_dir == '':
     control_gvcf_dir = None
 else:
     control_gvcf_dir = args.control_gvcf_dir if (args.control_gvcf_dir[-1] == "/") else (args.control_gvcf_dir + "/")
@@ -170,7 +170,7 @@ def get_running_workflows():
             json.dump(wf_arguments, f)
 
         # Submit the workflow for the current file
-        generate_name = sample_id + "-"
+        generate_name = sample_id.replace('_', '') + "-"
         workflow = {
             "namespace": "early-check-rs-1",
             "serverDryRun": False,