Updated workflow IDs in wgs_qc_wf_tools

wgs_qc_wf_tools/v1.0/create_step_2_config.py

@@ -20,7 +20,7 @@
     required = True
 )
 parser.add_argument(
-    '--step_1_output_json',
+    '--step_1_outputs_json',
     help = 'S3 path to JSON file containing outputs from Step 1',
     type = str,
     required = True

wgs_qc_wf_tools/v1.0/entrypoint.sh

@@ -37,7 +37,7 @@ if ["$task" == "launch_step_1"]; then
         exit 
     fi
     if [ -z "$workflow_id" ]; then
-        workflow_id="3796246"
+        workflow_id="3565858"
     fi
 
     # Launch Step 1
@@ -66,7 +66,7 @@ if ["$task" == "launch_step_2"]; then
         minimum_ancestry_sample_count=50
     fi
     if [ -z "$workflow_id" ]; then
-        workflow_id="3796246"
+        workflow_id="5499609"
     fi
 
     # Create Step 2 config files

wgs_qc_wf_tools/v1.0/start_run.py

@@ -2,9 +2,16 @@
 import boto3
 from datetime import datetime
 import json
+import os
 
 # Get arguments
 parser = argparse.ArgumentParser()
+parser.add_argument(
+    '--run_metadata_output_dir',
+    help='Directory where metadata about the run will be output',
+    type = str,
+    required = True
+)
 parser.add_argument(
     '--aws_access_key_id',
     help='AWS access key ID for profile used to run workflow',
@@ -95,6 +102,9 @@
 )
 args = parser.parse_args()
 
+run_metadata_output_dir = args.run_metadata_output_dir if (args.run_metadata_output_dir[-1] == "/") else (args.run_metadata_output_dir + "/")
+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)
 omics = session.client('omics')
@@ -119,3 +129,6 @@
     retentionMode=args.retentionMode
 )
 
+with open("{}{}_metadata.json".format(run_metadata_output_dir, args.name), 'w', encoding='utf-8') as f:
+    json.dump(response, f)
+