Update example script.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index ad87207921fea4ce272d80af67b9ffe50e3e82df..6a18accc991c8564b24a6a320c5b57df7b71b7a0 100755 (executable)
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -7,12 +7,15 @@ go install
 lightning build-docker-image
 arv keep docker lightning-runtime
 
+priority=501
 project=su92l-j7d0g-jzei0m9yvgauhjf
+ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
 gvcf=su92l-4zz18-bgyq36m6gctk63q
 info=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
 tags=su92l-4zz18-92bx4zjg5hgs3yc
 
+genome=$(lightning ref2genome -project ${project} -priority ${priority} -ref ${ref_fa})
+fasta=$(lightning vcf2fasta   -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})
 unfiltered=$(
     lightning import       -project ${project} \
        -tag-library ${tags}/tagset.fa.gz \