check empty files

00-rules/filter_samples.smk

@@ -42,13 +42,9 @@ rule clean_pcrerr_samples:
     params:
          r=config["clean_pcrerr_samples"]["r"]         
     shell:
-        '''
-        if [[ -s {input} ]]
-        then
-            obiclean -r {params.r} {input} > {output} 2> {log}
-        else
-            touch {output} 2> {log}
-        fi
+        '''if [[ -s {input} ]] ;
+        then obiclean -r {params.r} {input} > {output} 2> {log} ;
+        else touch {output} 2> {log} ; fi
         '''
 
 ### Remove sequence which are classified as 'internal' by obiclean