check empty files

00-rules/filter_samples.smk

@@ -42,12 +42,14 @@ 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
 rule rm_internal_samples: