Handle N in ref.

[lightning.git] / example-su92l-1kg.sh

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index 7bd631b9eb6dfac8fdbdb8d129cb312fcad342c5..1e5ecbc1b348535695714d096c7e88c173202c24 100755 (executable)
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -7,30 +7,21 @@ go install
 lightning build-docker-image
 arv keep docker lightning-runtime
 
+priority=501
 project=su92l-j7d0g-jzei0m9yvgauhjf
-gvcf=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
-tags=su92l-4zz18-92bx4zjg5hgs3yc
+ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
+gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
+info=su92l-4zz18-ykpcoea5nisz74f
+tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
 
-unfiltered=$(
-    lightning import       -project ${project} \
-       -tag-library ${tags}/tagset.fa.gz \
-       ${fasta})
-unfiltered=su92l-4zz18-fcyucnod8y4515p/library.gob
-filtered=$(
-    lightning filter       -project ${project} \
-       -i ${unfiltered} \
-       -min-coverage 0.9 -max-variants 30)
-numpy=$(
-    lightning export-numpy -project ${project} \
-       -i ${filtered})
-pca=$(
-    lightning pca          -project ${project} \
-       -i ${numpy})
-plot=$(
-    lightning plot         -project ${project} \
-       -i ${pca} \
-       -labels-csv ${gvcf}/sample_info.csv \
-       -sample-fasta-dir ${fasta})
+genome=$(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} -priority ${priority} -tag-library ${tagset} -skip-ooo=true ${fasta})
+stats=$(lightning      stats        -project ${project} -priority ${priority} -i ${unfiltered})
+filtered=$(lightning   filter       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")
+#numpy=$(lightning     export-numpy -project ${project} -priority ${priority} -i ${filtered} -one-hot)
+#pca=$(lightning       pca-py       -project ${project} -priority ${priority} -i ${numpy})
+pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${filtered} -one-hot)
+plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
 echo ${plot%%/*}