# HG changeset patch
# User estrain
# Date 1558374936 14400
# Node ID 53b629d3da6866a1861a0ad9f9cdddaf2f618b2b
# Parent  65cb7bb11e6b05f9034a8f420efd6f71f0e6b7ad
Uploaded

diff -r 65cb7bb11e6b -r 53b629d3da68 srst2v2.xml
--- a/srst2v2.xml	Sun May 19 11:24:38 2019 -0400
+++ b/srst2v2.xml	Mon May 20 13:55:36 2019 -0400
@@ -15,7 +15,7 @@
             ln -s $paired_conditional.fastq1 sample_1.fastq;
             ln -s $paired_conditional.fastq2 sample_2.fastq;
           #end if
-        #else if $paired_conditional.sPaired == "paired_coll" 
+	#else if $paired_conditional.sPaired == "paired_coll" 
 	  #if $paired_conditional.coll.forward.is_of_type("fastq.gz")
             zcat $paired_conditional.coll.forward > sample_1.fastq;
             zcat $paired_conditional.coll.reverse > sample_2.fastq;
@@ -26,7 +26,7 @@
             ln -s $paired_conditional.coll.forward sample_1.fastq;
             ln -s $paired_conditional.coll.reverse sample_2.fastq;
           #end if
-        #else if $paired_conditional.sPaired == "single"
+	#else if $paired_conditional.sPaired == "single"
 	  #if $paired_conditional.fastq1.is_of_type("fastq.gz")
             zcat $paired_conditional.fastq1 > sample_1.fastq;
 	  #else if $paired_conditional.fastq1.is_of_type("fastqsanger.gz")
@@ -39,7 +39,7 @@
         srst2
 
         #if $paired_conditional.sPaired == "single"
-            --input_se sample_1.fastq1
+            --input_se sample_1.fastq
         #else
             --input_pe sample_1.fastq sample_2.fastq
         #end if