priority=501
project=su92l-j7d0g-jzei0m9yvgauhjf
ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
-gvcf=su92l-4zz18-bgyq36m6gctk63q
+ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
+gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
info=su92l-4zz18-ykpcoea5nisz74f
-tags=su92l-4zz18-92bx4zjg5hgs3yc
-
-genome=$(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 \
- ${fasta})
-filtered=$(
- 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 ${info}/sample_info.csv \
- -sample-fasta-dir ${fasta})
+tagset=su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz
+
+genome=$(lightning ref2genome -project ${project} -priority ${priority} -ref ${ref_fa}) ; echo genome=${genome}
+fasta=$(lightning vcf2fasta -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf}) ; echo fasta=${fasta}
+# fasta=su92l-4zz18-9nq05jifgz7iult
+
+ref37_lib=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -include-no-calls ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
+# 539s
+
+unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta}) ; echo unfiltered=${unfiltered}
+# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
+
+merged=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib}) ; echo merged=${merged}
+# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
+# 2400s
+
+exportvcf=$(lightning export -project ${project} -priority ${priority} -i ${merged} -output-format vcf -ref /mnt/su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz -output-bed export.bed) ; echo exportvcf=${exportvcf}
+# exportvcf=su92l-4zz18-gz4svr6zyvipueu/export.csv
+# 5506s
+
+stats=$(lightning stats -project ${project} -priority ${priority} -i ${merged}) ; echo stats=${stats}
+
+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}
+
+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 ${fasta})
echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
echo ${plot%%/*}
+
+numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${filtered} -one-hot)