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317 remove excess header values in VCF extract #7786

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merged 5 commits into from
Apr 15, 2022
Merged

317 remove excess header values in VCF extract #7786

merged 5 commits into from
Apr 15, 2022

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RoriCremer
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@RoriCremer RoriCremer commented Apr 14, 2022 •
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gatk-bot commented Apr 14, 2022 •
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Travis reported job failures from build 38875
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38875.13 logs
unit openjdk8 38875.3 logs

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gatk-bot commented Apr 14, 2022 •
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Travis reported job failures from build 38877
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38877.13 logs
unit openjdk8 38877.3 logs

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gatk-bot commented Apr 14, 2022 •
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Travis reported job failures from build 38879
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38879.13 logs
unit openjdk8 38879.3 logs

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gatk-bot commented Apr 14, 2022 •
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Travis reported job failures from build 38881
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38881.13 logs
unit openjdk8 38881.3 logs

@RoriCremer RoriCremer force-pushed the rc-vs-317-remove-excess-headers branch from da8a97a to ff6a114 Compare April 15, 2022 00:57
@RoriCremer RoriCremer force-pushed the rc-vs-317-remove-excess-headers branch from c547147 to 45e4187 Compare April 15, 2022 01:02
@RoriCremer RoriCremer marked this pull request as ready for review April 15, 2022 01:04
@RoriCremer RoriCremer changed the title Rc vs 317 remove excess headers 317 remove excess header values in VCF extract Apr 15, 2022
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Travis reported job failures from build 38891
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38891.13 logs

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gatk-bot commented Apr 15, 2022 •
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Travis reported job failures from build 38893
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38893.13 logs
unit openjdk8 38893.3 logs

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gatk-bot commented Apr 15, 2022 •
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Travis reported job failures from build 38895
Failures in the following jobs:

Test Type JDK Job ID Logs
unit openjdk11 38895.13 logs
unit openjdk8 38895.3 logs
unit openjdk11 38895.13 logs
unit openjdk8 38895.3 logs
unit openjdk11 38895.13 logs
unit openjdk8 38895.3 logs

gbggrant
gbggrant approved these changes Apr 15, 2022
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Looks good.

.dockstore.yml
@@ -117,6 +117,7 @@ workflows:
branches:
- master
- ah_var_store
- rc-vs-317-remove-excess-headers
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Do we get rid of these before we merge the PR?

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Ideally yes, but with tests taking so long, sometimes we dont. It would be great to do a full clean up of all the extra branches in dockstore too

scripts/variantstore/wdl/GvsExtractCallset.wdl
@@ -15,7 +15,7 @@ workflow GvsExtractCallset {

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-add-AD-04112022/gatk-package-4.2.0.0-498-g1f53709-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-update-headers-04142022/gatk-package-4.2.0.0-497-gda8a97a-SNAPSHOT-local.jar"
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Should these directory have the jira ticket number embedded (to see if the work has been merged into ah_var_store and so we can assume the directory and jar is stale / unneeded).

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@mcovarr mcovarr Apr 15, 2022 •
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Yeah I agree that would be good. With the combo of embedding the ticket number in the branch name and the "copy your custom GATK jar" script that Kristian shared the other day we seem to get that.

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I like this! Maybe post-Charlie we can consolidate a set of rules for jars? It's certainly too haphazard now

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Ran this jar on the MSSNG call set and compared one of the output VCFs with that generated using the original (default) jar - differences found were as expected:

wm944-c33:gatk ggrant$ diff mssng_6_new_updated_header.vcf mssng_6_original.vcf 
1a2
> ##FILTER=<ID=EXCESS_ALLELES,Description="Site has an excess of alternate alleles based on the input threshold (default is 6)">
3a5
> ##FILTER=<ID=NAY,Description="Considered a NAY in the Yay, Nay, Grey table">
17a20,21
> ##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
> ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

mcovarr
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LGTM once Travis is happy. 👍

scripts/variantstore/wdl/GvsExtractCallset.wdl
@@ -15,7 +15,7 @@ workflow GvsExtractCallset {

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-add-AD-04112022/gatk-package-4.2.0.0-498-g1f53709-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-update-headers-04142022/gatk-package-4.2.0.0-497-gda8a97a-SNAPSHOT-local.jar"
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@mcovarr mcovarr Apr 15, 2022 •
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Yeah I agree that would be good. With the combo of embedding the ticket number in the branch name and the "copy your custom GATK jar" script that Kristian shared the other day we seem to get that.

@RoriCremer RoriCremer merged commit 1387d47 into ah_var_store Apr 15, 2022
@RoriCremer RoriCremer deleted the rc-vs-317-remove-excess-headers branch April 15, 2022 18:29
This was referenced Mar 17, 2023
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@gbggrant gbggrant gbggrant approved these changes

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@RoriCremer @gatk-bot @gbggrant @mcovarr