--- a/stacks_shortreads.xml	Mon Jul 01 11:02:39 2019 -0400
+++ b/stacks_shortreads.xml	Mon Sep 30 14:16:13 2019 -0400
@@ -12,6 +12,10 @@
 
 mkdir stacks_inputs stacks_outputs &&
 
+#if $output_log
+    ln -s '$output_log' stacks_outputs/process_shortreads.log &&
+#end if
+
 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
 $link_command
 
@@ -29,9 +33,6 @@
 $options_advanced.mate_pair
 $options_advanced.no_overhang
 
-#if $output_log
-    && mv stacks_outputs/process_shortreads.log $output_log
-#end if
 @PROCESS_FASTQ_POSTPROC@
     ]]></command>
 
@@ -82,13 +83,14 @@
             </param>
             <param name="input_type|barcode_encoding" value="--inline_null"/>
             <param name="barcode" value="procrad/barcodes"/>
-            <param name="capture" value="true"/>
+            <param name="capture" value="-D"/>
             <param name="no_read_trimming" value="--no_read_trimming" />
             <param name="mate_pair" value="--mate-pair" />
             <param name="no_overhang" value="--no_overhang" />
             <param name="outype" value="gzfastq"/>
             <param name="add_log" value="yes" />
             <assert_command>
+                <has_text text="-D" />
                 <has_text text="--no_read_trimming" />
                 <has_text text="--mate-pair" />
                 <has_text text="--no_overhang" />