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Workflow to re-scatter and then merge "problematic" intervals from ExtractCallset [VS-209] #7495

Merged
merged 45 commits into from
Oct 14, 2021
Merged

Workflow to re-scatter and then merge "problematic" intervals from ExtractCallset [VS-209] #7495

merged 45 commits into from
Oct 14, 2021

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rsasch
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@rsasch rsasch commented Oct 7, 2021

@rsasch
run SplitIntervals with localization enabled
acf1549
@rsasch
dockstore
7cdbf85
@rsasch
removed retries and updated gatk docker for ExtractTask
1145547
@rsasch
make use of retry with more memory and associated env variables
67d5fc6
@rsasch
more fun with memory env vars
6b8b573
@rsasch
Merge branch 'ah_var_store' into rsa_split_intervals
e48fad1
@rsasch
roll back other changes to GvsExtractCallset besides SplitIntervals l…
c1d5d4b 
…ocalization
@rsasch
added split_intervals_disk_size_override
6f8c0d2
@rsasch
try to make the right thing parameterized
75e6250
@rsasch
Merge branch 'ah_var_store' into rsa_split_intervals
8b10698
@rsasch
add service account json support to CreateManifest
3014290
@rsasch
copy-paste error
6004773
@rsasch
added wdl for sharded shards and associated python script
9856572
@rsasch
added for realsies
9989624
@rsasch
dockstore
450b2ee
@rsasch
minor tweaks
d2ffbef
@rsasch
variable name fix
9293c98
@rsasch
use range correctly
8c35677
@rsasch
right docker
ee9c96e
@rsasch
d'oh, forgot to set OUTPUT_GCS_DIR in ExtractTask
c678035
@rsasch
try without indexes
5910ee6
@rsasch
try without indexes input
8bccff9
@rsasch
try without indexes input
647b5dd
@rsasch
try without indexes input again
46ee9e2
@rsasch
turns out we don't need the index files to pass to GatherVcfsCloud
b43ade8
@rsasch
added merge_disk_override
da61b5a
@rsasch
change handling of merge_disk_override
9f42f59
@rsasch
renamed workflow, added to dockstore
8cc8cc5
@rsasch
first stab at knitting things together
3902183
@rsasch
fixing up paths
7d0d093
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gatk-bot commented Oct 7, 2021

Travis reported job failures from build 36352
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 36352.12 logs

ahaessly
ahaessly approved these changes Oct 12, 2021
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one change

scripts/variantstore/wdl/GvsRescatterCallsetInterval.wdl Outdated Show resolved Hide resolved
@rsasch rsasch requested a review from ahaessly October 12, 2021 18:15
@rsasch rsasch merged commit 10444d1 into ah_var_store Oct 14, 2021
@rsasch rsasch deleted the rsa_rescattering_wf branch October 14, 2021 23:49
This was referenced Mar 17, 2023
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@kcibul kcibul kcibul approved these changes

@ahaessly ahaessly Awaiting requested review from ahaessly

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@rsasch @gatk-bot @kcibul @ahaessly