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Create workflow to create and populate alt_allele table [VS-51] #7426

Merged
merged 24 commits into from
Sep 9, 2021
Merged

Create workflow to create and populate alt_allele table [VS-51] #7426

merged 24 commits into from
Sep 9, 2021

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rsasch
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@rsasch rsasch commented Aug 19, 2021

@rsasch
messy first stab
a81d5f1
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
4ea4904
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
6a88c43
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
0758d1e
@rsasch
added WDL to parallize loading alt_allele from vet tables
f562d35
@rsasch
fixed bugs, added new docker image
a59f5ec
@rsasch
add dockstore integration
73811ff
@rsasch
typo
96dc0dc
@rsasch
revenge of the typo
5be2ee5
@rsasch
fun with docker_build and scattering
ce19869
@rsasch
fun with docker_build and scattering
bd42100
@rsasch
ugh running things in docker
c75d64b
@rsasch
futzing
b1e92f4
@rsasch
updated QUICKSTART readme and made input parameter names consistent
dd6e735
@rsasch
fixed up Docker paths
b50d525
@rsasch
more futzing
1f33c5a
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
58c9be6
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
19848aa
@rsasch
Merge branch 'ah_var_store' into rsa_alt_allele_script
2ea1830
kcibul
kcibul requested changes Sep 3, 2021
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I think there's a race condition in here that needs to be looked at (See comments about table creation)

scripts/variantstore/wdl/GvsCreateAltAllele.wdl Outdated Show resolved Hide resolved
scripts/variantstore/wdl/extract/populate_alt_allele_table.py Outdated Show resolved Hide resolved
@rsasch rsasch requested a review from kcibul September 8, 2021 14:24
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gatk-bot commented Sep 8, 2021

Travis reported job failures from build 35880
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 35880.12 logs

kcibul
kcibul approved these changes Sep 8, 2021
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looks great!

@rsasch rsasch merged commit 80e2524 into ah_var_store Sep 9, 2021
@rsasch rsasch deleted the rsa_alt_allele_script branch September 9, 2021 17:59
RoriCremer pushed a commit that referenced this pull request Sep 20, 2021
@rsasch @RoriCremer
Create workflow to create and populate alt_allele table [VS-51] (#7426)
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This was referenced Mar 17, 2023
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@RoriCremer RoriCremer RoriCremer left review comments

@kcibul kcibul kcibul approved these changes

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@rsasch @gatk-bot @kcibul @RoriCremer