# HG changeset patch
# User greg
# Date 1700765853 0
# Node ID d10799246957beeec9bb16cd97111ece987020af
# Parent  e6451ad3db70a6f16e6d3196f4e13e5d748d6925
Uploaded

diff -r e6451ad3db70 -r d10799246957 cfsan_snp_pipeline_filter_snp_regions.xml
--- a/cfsan_snp_pipeline_filter_snp_regions.xml	Fri Oct 13 13:09:05 2023 +0000
+++ b/cfsan_snp_pipeline_filter_snp_regions.xml	Thu Nov 23 18:57:33 2023 +0000
@@ -11,7 +11,7 @@
     #set reference = $reference_cond.reference
 #end if
 mkdir -p ./samples/sample/ &&
-ln -s '$calls' ./samples/sample/var.flt.vcf &&
+cp '$calls' ./samples/sample/var.flt.vcf &&
 echo "\$PWD/samples/sample" > ./alignment.txt &&
 cfsan_snp_pipeline filter_regions ./alignment.txt '$reference' &&
 cp ./samples/sample/var.flt_preserved.vcf '$filcalls' &&