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Clean up optional and inconsistently named inputs [VS-294] [VS-218] #7715

Merged
merged 36 commits into from
Mar 21, 2022
Merged

Clean up optional and inconsistently named inputs [VS-294] [VS-218] #7715

merged 36 commits into from
Mar 21, 2022

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rsasch
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@rsasch rsasch commented Mar 10, 2022 •
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  • hard-code inputs that shouldn't be override-able
  • name inputs consistently

Closes

rsasch added 28 commits March 3, 2022 13:43
@rsasch
GvsAssignIds
c1a4a70
@rsasch
more GvsAssignIds
fd6631f
@rsasch
GvsImportGenomes
36afed1
@rsasch
GvsAssignIds and GvsImportGenomes
900b03b
@rsasch
bit more for GvsImportGenomes
f1244a6
@rsasch
gatk_override for GvsImportGenomes
8b6c26e
@rsasch
neaten GvsImportGenomes
24cf6f5
@rsasch
fix gatk for GvsImportGenomes
cac91e3
@rsasch
fix gatk for GvsImportGenomes
5975cf1
@rsasch
GvsCreateAltAllele
e00fac7
@rsasch
GvsCreateFilterSet
7663e4c
@rsasch
starting on GvsCreateFilterSet
0863de0
@rsasch
moreGvsCreateFilterSet
9f411e5
@rsasch
even more GvsCreateFilterSet
a037dd8
@rsasch
fix sample_info table name
bf2df5c
@rsasch
fix typo in reference path
ec4134c
@rsasch
GvsPrepareRangesCallset
4dc643a
@rsasch
wrong dockstore -- d'oh
e1ee0d9
@rsasch
modify readme
95d80bd
@rsasch
cleaned up extract, quickstart md for prepare and extract
9681e5d
@rsasch
remove default for extract_table_prefix
e6a7106
@rsasch
quickstart and typo fix
a535a5f
@rsasch
meta wdls
3d71b7d
@rsasch
more neatening
7c4dcbd
@rsasch
reodering
8349161
@rsasch
Merge branch 'ah_var_store' into rsa_optional_inputs
7603cbc
@rsasch
Merge branch 'ah_var_store' into rsa_optional_inputs
b3a0a09
@rsasch
unused inputs for GvsExtractCohortFromSampleNames
1d1a1c0
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gatk-bot commented Mar 14, 2022 •
edited
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Travis reported job failures from build 38100
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38100.12 logs
integration openjdk8 38100.2 logs
integration openjdk8 38100.2 logs
integration openjdk11 38100.12 logs
integration openjdk8 38100.2 logs
integration openjdk11 38100.12 logs
integration openjdk11 38100.12 logs
integration openjdk11 38100.12 logs
integration openjdk8 38100.2 logs
integration openjdk11 38100.12 logs
integration openjdk8 38100.2 logs

@rsasch rsasch changed the title Clean up optional and inconsistently named inputs [VS-294] Clean up optional and inconsistently named inputs [VS-294] [VS-218] Mar 17, 2022
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gatk-bot commented Mar 18, 2022 •
edited
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Travis reported job failures from build 38166
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38166.12 logs
integration openjdk8 38166.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38174
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38174.12 logs
integration openjdk8 38174.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38177
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38177.12 logs
integration openjdk8 38177.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38179
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38179.12 logs
integration openjdk8 38179.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38183
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38183.12 logs
integration openjdk8 38183.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38185
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38185.12 logs
integration openjdk8 38185.2 logs

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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38187
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38187.12 logs
integration openjdk8 38187.2 logs

@rsasch rsasch merged commit db6b15f into ah_var_store Mar 21, 2022
@rsasch rsasch deleted the rsa_optional_inputs branch March 21, 2022 22:21
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gatk-bot commented Mar 21, 2022 •
edited
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Travis reported job failures from build 38191
Failures in the following jobs:

Test Type JDK Job ID Logs
integration openjdk11 38191.12 logs
integration openjdk8 38191.2 logs

This was referenced Mar 17, 2023
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@kcibul kcibul kcibul left review comments

@RoriCremer RoriCremer RoriCremer approved these changes

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@rsasch @gatk-bot @kcibul @RoriCremer