From 1d39c643fa17faea594357542a905bcafef3725d Mon Sep 17 00:00:00 2001
From: Trestan Pillonel <trestan.pillonel@chuv.ch>
Date: Thu, 7 Nov 2024 15:41:53 +0100
Subject: [PATCH] deal with no resistance gene found

---
 rules/report_generation/report_resistance.rules | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/rules/report_generation/report_resistance.rules b/rules/report_generation/report_resistance.rules
index d7fedf6..b44d11a 100644
--- a/rules/report_generation/report_resistance.rules
+++ b/rules/report_generation/report_resistance.rules
@@ -63,5 +63,5 @@ rule resistance_detailed_table:
     shell: 
         """
         head -n1 {input[0]} >> {output}
-        cat {input} | grep -v ORF_ID >> {output}
+        cat {input} | grep -v ORF_ID >> {output} || true
         """