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[GEN-1026] Output annotation error report #544

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merged 6 commits into from
Jan 11, 2024
+10 −2
Merged

[GEN-1026] Output annotation error report #544

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cc081a1
update java version to match gn annotator.jar file, change tag versio…
rxu17 Jan 5, 2024
00f527e
use newer version of annotator.jar
rxu17 Jan 8, 2024
5c955cd
define error report dir
rxu17 Jan 8, 2024
d7b3bd0
add error dir changes to tests
rxu17 Jan 8, 2024
2267c4a
lint
rxu17 Jan 8, 2024
b3d6491
comment out version until we can pull from config file
rxu17 Jan 11, 2024
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use newer version of annotator.jar
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@rxu17
rxu17 committed Jan 8, 2024
commit 00f527e5628040418b345f65f9cb3976e366564c
2 changes: 2 additions & 0 deletions genie/process_mutation.py
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Original file line number Diff line number Diff line change
@@ -202,12 +202,14 @@ def process_mutation_workflow(
"syn22053204",
ifcollision="overwrite.local",
downloadLocation=genie_config["genie_annotation_pkg"],
version=1, #TODO: This should pull from a config file in the future
)
# Genome Nexus Jar file
syn.get(
"syn22084320",
ifcollision="overwrite.local",
downloadLocation=genie_config["genie_annotation_pkg"],
version=13, #TODO: This should pull from a config file in the future
)

annotated_maf_path = annotate_mutation(