Mercurial > repos > greg > cfsan_snp_pipeline_filter_snp_regions

changeset 3:d10799246957 draft default tip

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Uploaded
author greg
date Thu, 23 Nov 2023 18:57:33 +0000
parents e6451ad3db70
children
files cfsan_snp_pipeline_filter_snp_regions.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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' &&