Mercurial > repos > greg > cfsan_snp_pipeline_filter_snp_regions

comparison cfsan_snp_pipeline_filter_snp_regions.xml @ 3:d10799246957 draft default tip

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author greg
date Thu, 23 Nov 2023 18:57:33 +0000
parents e6451ad3db70
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2:e6451ad3db70 3:d10799246957
9 #set reference = $reference_cond.reference.fields.path 9 #set reference = $reference_cond.reference.fields.path
10 #else: 10 #else:
11 #set reference = $reference_cond.reference 11 #set reference = $reference_cond.reference
12 #end if 12 #end if
13 mkdir -p ./samples/sample/ && 13 mkdir -p ./samples/sample/ &&
14 ln -s '$calls' ./samples/sample/var.flt.vcf && 14 cp '$calls' ./samples/sample/var.flt.vcf &&
15 echo "\$PWD/samples/sample" > ./alignment.txt && 15 echo "\$PWD/samples/sample" > ./alignment.txt &&
16 cfsan_snp_pipeline filter_regions ./alignment.txt '$reference' && 16 cfsan_snp_pipeline filter_regions ./alignment.txt '$reference' &&
17 cp ./samples/sample/var.flt_preserved.vcf '$filcalls' && 17 cp ./samples/sample/var.flt_preserved.vcf '$filcalls' &&
18 cp ./samples/sample/var.flt_removed.vcf '$excludes' 18 cp ./samples/sample/var.flt_removed.vcf '$excludes'
19 ]]></command> 19 ]]></command>