Merge pull request #1416 from mskcc/hotfix/v2_nucleo_agg

Hotfix/v2 nucleo agg
mskcc · Feb 11, 2025 · a69883e · a69883e
2 parents 608a1eb + 52ecbee
commit a69883e
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Showing 4 changed files with 8 additions and 3 deletions.
diff --git a/beagle/__init__.py b/beagle/__init__.py
@@ -1 +1 @@
-__version__ = "1.91.5"
+__version__ = "1.91.6"
diff --git a/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py b/runner/operator/access/v2_1_0/qc/access_nucleo_qc.py
@@ -67,6 +67,7 @@ def get_jobs(self):
                     "name": "Access V2 Nucleo QC: %s, %i of %i" % (self.request_id, i + 1, len(sample_inputs)),
                     "app": self.get_pipeline_id(),
                     "inputs": job,
+                    "output_metadata": output_metadata,
                     "tags": {settings.REQUEST_ID_METADATA_KEY: self.request_id, "cmoSampleId": job["sample_name"]},
                 }
             )

diff --git a/runner/operator/access/v2_1_0/qc/input_template.json.jinja2 b/runner/operator/access/v2_1_0/qc/input_template.json.jinja2
@@ -79,5 +79,9 @@
     "fragment_count": 1,
     "filter_duplicate": 0,
     "omaf": true,
-    "generic_counting": true
+    "generic_counting": true,
+    "athena_thresholds": [250,500,1000,1500,2000],
+    "athena_threshold": 500,
+    "athena_summary": true,
+    "athena_cores": 4
 }
diff --git a/runner/operator/access/v2_1_0/qc_agg/access_nucleo_qc_agg.py b/runner/operator/access/v2_1_0/qc_agg/access_nucleo_qc_agg.py
@@ -96,7 +96,7 @@ def get_qc_outputs(self):
         input = self.construct_sample_input(most_recent_runs_for_request)
         sample_list = []
         for single_run in most_recent_runs_for_request:
-            sample_list.append(single_run.tags["cmoSampleId"][0])
+            sample_list.append(single_run.output_metadata[settings.CMO_SAMPLE_NAME_METADATA_KEY])
         return input, sample_list
 
     def process_listing(self, listing, name):