Update cutadapt.rules

workflow/rules/cutadapt.rules

@@ -49,16 +49,18 @@ rule cutadapt:
     	tmp="{output}"
     	outfiles=($tmp)	
     
+       mode="{params.mode}"
+
         # add mode and adapter sequences
-        cmd+=" cutadapt -j {threads} -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options}  "
+        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]}} ${{infiles[0]}}"
         fi
         #run command
-        eval "${{cmd}} > {log.out}"
+        eval "${{cmd}} > {log}"
 
         """