Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
filtered=$(lightning filter -project ${project} -priority ${priority} -i ${merged} -min-coverage "0.9" -max-variants "30") ; echo filtered=${filtered}
-annotations=$(lightning annotate -project ${project} -priority ${priority} -i ${merged}) ; echo annotated=${annotated}
+annotations=$(lightning annotate -project ${project} -priority ${priority} -i ${merged}) ; echo annotations=${annotations}
pca=$(lightning pca-go -project ${project} -priority ${priority} -i ${filtered} -one-hot) ; echo pca=${pca}
plot=$(lightning plot -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})