update QC pass display

broadinstitute · May 23, 2024 · 82073a7 · 82073a7
1 parent 80ddbf4
commit 82073a7
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/docker/lr-malaria-reports/report-files/report_gen.py b/docker/lr-malaria-reports/report-files/report_gen.py
@@ -652,6 +652,10 @@ def create_report(sample, analysis, fastQC):
             arg_dict['aligned_read_length_median'], arg_dict['read_qual_median']]
 
     qc_pass = arg_dict["qc_pass"]
+    if (qc_pass == "true"):
+        qc_pass = "PASS"
+    elif (qc_pass == "false"):
+        qc_pass = "FAIL"
 
     # Check if drug resistance report is provided
     if not arg_dict['drug_resistance_text'] or arg_dict['drug_resistance_text'] == "None":