# HG changeset patch
# User dfornika
# Date 1548110790 18000
# Node ID 84a619014025e3920b55946d3d47625f5516a8db
# Parent  b9eacd069df6c6a135797809e55e7ebc81ba0609
planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty

diff -r b9eacd069df6 -r 84a619014025 snippy.xml
--- a/snippy.xml	Mon Jan 21 15:46:37 2019 -0500
+++ b/snippy.xml	Mon Jan 21 17:46:30 2019 -0500
@@ -54,11 +54,11 @@
 
         #import re
 	#if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.element_identifier)
+	    #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.forward.name)
 	#else
             #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
 	#end if
-        mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+        mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
 
         tar -czf out.tgz ${dir_name}