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 -project ${project} -priority ${priority} -i ${numpy})
+#numpy=$(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%%/*}