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Fixes to CreateFilterSet and ExtractCallset from 30K run #7423

Merged
merged 31 commits into from
Aug 19, 2021
Merged

Fixes to CreateFilterSet and ExtractCallset from 30K run #7423

merged 31 commits into from
Aug 19, 2021

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rsasch
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@rsasch rsasch commented Aug 18, 2021

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ahaessly and others added 28 commits August 11, 2021 13:46
@ahaessly
add new wdl
0c94ba2
@ahaessly
fix snp recal parameters
7f66d6e
@ahaessly
fix format
892463d
@ahaessly
deubg dockstore
9d5e1b5
@ahaessly
debug dockstore
672868f
@ahaessly
update more params
f72fb6e
@rsasch
Merge branch 'ah_var_store' into ah_filter_fixes
f0a2157
@rsasch
added SNP_VQSR_machine_mem_gb and excluded_sites_bed to SNPsVariantRe…
3082c3a 
…calibratorCreateModel
@rsasch
removed sample files
03eb80b
@rsasch
use service_account.json for SplitIntervals call
54d15b5
@rsasch
please, dockstore
4dc4255
@rsasch
more dockstore negotiation
7e4155c
@rsasch
more dockstore negotiation (2)
13a58bb
@rsasch
more dockstore negotiation (3)
fec1f05
@ahaessly
debug yml
eba7ccf
@ahaessly
debug yml
4483ead
@ahaessly
copied yml from another branch and modified
90d57bb
@ahaessly
remove branch
55169f4
@rsasch
try passing the project_id with the service_account.json
0d3d478
@rsasch
try passing the project_id with the service_account.json
ffadfed
@rsasch
Merge branch 'ah_filter_fixes' of https://github.com/broadinstitute/gatk
5bb411e 
 into ah_filter_fixes
@rsasch
try taking out non-localization from SplitIntervals
00d26d7
@rsasch
as long as I'm testing things, just remove all other calls so I'm onl…
b0fc4ff 
…y testing Split Intervals
@rsasch
as long as I'm testing things, just comment out all other calls so I'…
d430f1f 
…m only testing SplitIntervals
@rsasch
add back in localization meta params
6ab0ba8
@rsasch
changed file sizes from ints to floats to support larger values
462359c
@rsasch
Merge branch 'ah_var_store' into ah_filter_fixes
5fe26c8
@rsasch
fixes to CreateFilterSet and ExtractCallset from 30K run
9f007cf
ahaessly
ahaessly approved these changes Aug 18, 2021
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This all looks great! I would also like to fix the disk override parameters so that they work correctly. Let's chat about this face to face.

ahaessly
ahaessly approved these changes Aug 19, 2021
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one suggestion. either way 👍

scripts/variantstore/wdl/GvsCreateFilterSet.wdl Outdated Show resolved Hide resolved
@rsasch rsasch merged commit c89c82b into ah_var_store Aug 19, 2021
@rsasch rsasch deleted the ah_rsa_30K_fixes branch August 19, 2021 18:23
@rsasch rsasch mentioned this pull request Aug 20, 2021
Merged
ahaessly pushed a commit that referenced this pull request Aug 27, 2021
@rsasch @ahaessly
Fixes to CreateFilterSet and ExtractCallset from 30K run (#7423)
9244cdf
This was referenced Mar 17, 2023
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@rsasch @ahaessly