Added aws_region_name parameter to wgs_qc_wf_tools v1.0

RTIInternational · Sep 25, 2024 · f8c9e1d · f8c9e1d
1 parent 9838159
commit f8c9e1d
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Showing 4 changed files with 22 additions and 2 deletions.
diff --git a/wgs_qc_wf_tools/v1.0/Dockerfile b/wgs_qc_wf_tools/v1.0/Dockerfile
@@ -29,3 +29,4 @@ RUN chmod 755 /opt/start_run.py
 
 # Set the entry point command
 ENTRYPOINT [ "/opt/entrypoint.sh" ]
+
diff --git a/wgs_qc_wf_tools/v1.0/create_step_2_config.py b/wgs_qc_wf_tools/v1.0/create_step_2_config.py
@@ -19,6 +19,12 @@
     type = str,
     required = True
 )
+parser.add_argument(
+    '--aws_region_name',
+    help='AWS region in which step 1 of the workflow was run',
+    type = str,
+    required = True
+)
 parser.add_argument(
     '--step_1_outputs_json',
     help = 'S3 path to JSON file containing outputs from Step 1',
@@ -51,7 +57,7 @@
     step_1_output_bucket = result.group(1)
     step_1_output_json = result.group(2)
     local_step_1_output_json = '{}step_1_outputs.json'.format(output_dir)
-    session = boto3.Session(aws_access_key_id=args.aws_access_key_id, aws_secret_access_key=args.aws_secret_access_key)
+    session = boto3.Session(aws_access_key_id=args.aws_access_key_id, aws_secret_access_key=args.aws_secret_access_key, region_name=args.aws_region_name)
     s3 = session.resource('s3')
     my_bucket = s3.Bucket(step_1_output_bucket)
     my_bucket.download_file(step_1_output_json, local_step_1_output_json)

diff --git a/wgs_qc_wf_tools/v1.0/entrypoint.sh b/wgs_qc_wf_tools/v1.0/entrypoint.sh
@@ -18,6 +18,10 @@ if [ -z "$aws_secret_access_key" ]; then
     echo "aws_secret_access_key not provided, exiting!"
     exit
 fi
+if [ -z "$aws_region_name" ]; then
+    echo "aws_region_name not provided, exiting!"
+    exit
+fi
 # Assign default values if parameters not provided
 if [ -z "$role_arn" ]; then
     role_arn="arn:aws:iam::515876044319:role/service-role/OmicsWorkflow-20240601210363"
@@ -49,6 +53,7 @@ if [[ "$task" == "launch_step_1" ]]; then
         --run_metadata_output_dir $run_metadata_output_dir \
         --aws_access_key_id $aws_access_key_id \
         --aws_secret_access_key $aws_secret_access_key \
+        --aws_region_name $aws_region_name \
         --workflowId $workflow_id \
         --parameters $parameters \
         --name $name \
@@ -78,6 +83,7 @@ if [[ "$task" == "launch_step_2" ]]; then
     python3 /opt/create_step_2_config.py \
         --aws_access_key_id $aws_access_key_id \
         --aws_secret_access_key $aws_secret_access_key \
+        --aws_region_name $aws_region_name \
         --step_1_output_json $step_1_output_json \
         --output_dir $step_2_config_output_dir \
         --minimum_ancestry_sample_count $minimum_ancestry_sample_count
@@ -90,6 +96,7 @@ if [[ "$task" == "launch_step_2" ]]; then
             --run_metadata_output_dir $run_metadata_output_dir \
             --aws_access_key_id $aws_access_key_id \
             --aws_secret_access_key $aws_secret_access_key \
+            --aws_region_name $aws_region_name \
             --workflowId $workflow_id \
             --parameters $step_2_config \
             --name $name \

diff --git a/wgs_qc_wf_tools/v1.0/start_run.py b/wgs_qc_wf_tools/v1.0/start_run.py
@@ -24,6 +24,12 @@
     type = str,
     required = True
 )
+parser.add_argument(
+    '--aws_region_name',
+    help='AWS region in which to run workflow',
+    type = str,
+    required = True
+)
 parser.add_argument(
     '--workflowId',
     help='Healthomics ID of workflow',
@@ -106,7 +112,7 @@
 os.system("mkdir -p {}".format(run_metadata_output_dir))
 
 # Open AWS Healthomics session
-session = boto3.Session(aws_access_key_id=args.aws_access_key_id, aws_secret_access_key=args.aws_secret_access_key)
+session = boto3.Session(aws_access_key_id=args.aws_access_key_id, aws_secret_access_key=args.aws_secret_access_key, region_name=args.aws_region_name)
 omics = session.client('omics')
 
 # Read wf arguments