Mercurial > repos > greg > cfsan_snp_pipeline_filter_snp_regions
diff cfsan_snp_pipeline_filter_snp_regions.xml @ 3:d10799246957 draft default tip
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author | greg |
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date | Thu, 23 Nov 2023 18:57:33 +0000 |
parents | e6451ad3db70 |
children |
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--- 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' &&