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Small updates to GvsExtractCallset from beta callset, new workflow for re-scattered shards #7493

Merged
merged 27 commits into from
Oct 7, 2021
Merged

Small updates to GvsExtractCallset from beta callset, new workflow for re-scattered shards #7493

merged 27 commits into from
Oct 7, 2021

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rsasch
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@rsasch rsasch commented Oct 5, 2021

  • added split_intervals_disk_size_override parameter to GvsExtractCallset
  • added support for service account json to CreateManifest in GvsExtractCallset
  • GvsMergeScatteredCallsetShards.wdl and associated python script

@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
kcibul
kcibul approved these changes Oct 5, 2021
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lgtm -- but please check the comment about the range of range()

scripts/variantstore/wdl/GvsMergeScatteredCallsetShards.wdl Outdated Show resolved Hide resolved
scripts/variantstore/wdl/GvsMergeScatteredCallsetShards.wdl Show resolved Hide resolved
scripts/variantstore/wdl/extract/generate_ordered_paths.py Show resolved Hide resolved
scripts/variantstore/wdl/extract/generate_ordered_paths.py Show resolved Hide resolved
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gatk-bot commented Oct 5, 2021

Travis reported job failures from build 36299
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud openjdk11 36299.14 logs

@rsasch rsasch merged commit 6c927ae into ah_var_store Oct 7, 2021
@rsasch rsasch deleted the rsa_split_intervals branch October 7, 2021 14:24
This was referenced Mar 17, 2023
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@kcibul kcibul kcibul approved these changes

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@rsasch @gatk-bot @kcibul