From 548883a9d1f30e6f22e9f3960550bdecb372b939 Mon Sep 17 00:00:00 2001
From: Rachel  LEGENDRE <rachel.legendre@pasteur.fr>
Date: Mon, 13 Mar 2023 16:59:33 +0100
Subject: [PATCH] fix error with adapters in PE mode

---
 workflow/rules/cutadapt.rules | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/workflow/rules/cutadapt.rules b/workflow/rules/cutadapt.rules
index d9f95d5..deba3c3 100755
--- a/workflow/rules/cutadapt.rules
+++ b/workflow/rules/cutadapt.rules
@@ -22,8 +22,6 @@
 #########################################################################
 
 
-
-
 rule cutadapt:
     input:
         fastq = adapters_input_fastq
@@ -53,13 +51,14 @@ rule cutadapt:
     	
     	tmp="{output}"
     	outfiles=($tmp)	
-    
+        mode="{params.mode}"
+
         # add mode and adapter sequences
-        cmd+=" cutadapt -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options} -j {threads} "
+        cmd+=" cutadapt -${{mode}} {params.adapters} -m {params.min} -q {params.qual} {params.options} -j {threads} "
         # paired end or single end
         if [[ ${{#infiles[@]}} -eq 2 ]];
         then
-            cmd+=" -o ${{outfiles[0]}} -p ${{outfiles[1]}}  ${{infiles[0]}} ${{infiles[1]}} "
+            cmd+=" -${{mode^^}} {params.adapters} -o ${{outfiles[0]}} -p ${{outfiles[1]}}  ${{infiles[0]}} ${{infiles[1]}} "
         else
             cmd+=" -o ${{outfiles[0]}} ${{infiles[0]}}"
         fi
-- 
GitLab