Mercurial > repos > greg > cfsan_snp_pipeline_filter_snp_regions
comparison cfsan_snp_pipeline_filter_snp_regions.xml @ 3:d10799246957 draft default tip
Uploaded
author | greg |
---|---|
date | Thu, 23 Nov 2023 18:57:33 +0000 |
parents | e6451ad3db70 |
children |
comparison
equal
deleted
inserted
replaced
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> |