Configurable chromosome name pattern.

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

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index ad87207921fea4ce272d80af67b9ffe50e3e82df..abb696440d8065e020834c4f317f247683a9735b 100755 (executable)
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -7,30 +7,67 @@ go install
 lightning build-docker-image
 arv keep docker lightning-runtime
 
+priority=501
 project=su92l-j7d0g-jzei0m9yvgauhjf
-gvcf=su92l-4zz18-bgyq36m6gctk63q
+ref_fa=su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz
+ref37_fa=su92l-4zz18-caw3g2ji89jxix8/human_g1k_v37.fasta.gz
+gvcf=${HOME}/keep/by_id/su92l-4zz18-bgyq36m6gctk63q
 info=su92l-4zz18-ykpcoea5nisz74f
-fasta=su92l-4zz18-s3e6as6uzsoocsb
-tags=su92l-4zz18-92bx4zjg5hgs3yc
-
-unfiltered=$(
-    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 -save-incomplete-tiles ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+# ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
+# 539s
+
+ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref_fa}) ; echo ref38_lib=${ref38_lib}
+# ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
+
+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
+# unfiltered=su92l-4zz18-72ovi5qrderxudv/library.gob
+# 24674s @ pre-38e6e7c
+# unfiltered=su92l-4zz18-ywhkc1hgdzxwp5u/library.gob
+# 18497s @ 64vcpu bf0968a
+# _____s @ 32vcpu 83983ad
+
+
+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
+
+exporthgvs=$(lightning export       -project ${project} -priority ${priority} -i ${merged38} -output-format hgvs -ref /mnt/su92l-4zz18-u77iyyy7cb05xqv/hg38.fa.gz -output-bed hg38.bed) ; echo exporthgvs=${exporthgvs}
+# 
+# 
+
+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 ${merged})                                                            ; echo annotations=${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 ${fasta})
 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
 echo ${plot%%/*}
+
+
+merged38=$(lightning   merge        -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib})                                              ; echo merged38=${merged38}
+# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
+# 1602s
+# merged38=su92l-4zz18-5kcaci3hqzukjv2/library.gob
+# 2815s @ 83983ad
+
+numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${merged38})                                                          ; echo numpy=${numpy}
+# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
+# 6155s
+# pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
+comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}
+# comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv