# HG changeset patch
# User estrain
# Date 1569337420 14400
# Node ID 280e8868b85e29fbbe9b66b2d9d969133813f098
# Parent  e2b708d5c0d3411cf9ee5036fd991a57aa944c50
Fixed handling of paired reads

diff -r e2b708d5c0d3 -r 280e8868b85e skesa.xml
--- a/skesa.xml	Wed Oct 17 22:04:16 2018 -0400
+++ b/skesa.xml	Tue Sep 24 11:03:40 2019 -0400
@@ -14,10 +14,10 @@
         --fastq $jobtype.fastq1 
       #else if $jobtype.select == "fastq_fr"
         #set outname = $jobtype.fastq1.name
-        --fastq $jobtype.fastq1 --fastq $jobtype.fastq2
+        --fastq $jobtype.fastq1,$jobtype.fastq2
       #else if $jobtype.select == "fastq_pair"
         #set outname = $jobtype.coll.name
-        --fastq $jobtype.coll.forward --fastq $jobtype.coll.reverse
+        --fastq $jobtype.coll.forward,$jobtype.coll.reverse
       #end if
 
       #if $options.select=="advanced"