Total length should be at least genome_size to pass/fail samples

Snitkin-Lab-Umich · Feb 6, 2025 · 1c93466 · 1c93466
1 parent 3b9c741
commit 1c93466
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/QCD_report.smk b/QCD_report.smk
@@ -224,11 +224,12 @@ def summary(prefix, outdir):
     (QC_summary_temp7['Total # of contigs'] > config["max_contigs"]),
     (QC_summary_temp7['Total # of contigs'] < config["min_contigs"]),
     (QC_summary_temp7['Total length'] > config["assembly_length"]),
+    (QC_summary_temp7['Total length'] < config["genome_size"]), 
     (QC_summary_temp7['Coverage'] < config["coverage"]),
     (QC_summary_temp7['Total # of contigs'].isnull()),
     ]
 
-    status = ['FAIL', 'FAIL', 'FAIL', 'FAIL', "Run FAIL"]
+    status = ['FAIL', 'FAIL', 'FAIL', 'FAIL', 'FAIL', "Run FAIL"]
 
     QC_summary_temp7['QC Check'] = np.select(QC_check_condition, status, default='PASS')