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Non-GVS bits required for GVS [VS-971] #8362

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merged 5 commits into from
Jun 27, 2023
Merged

Non-GVS bits required for GVS [VS-971] #8362

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1c25535
renamed VCF header
mcovarr Jun 8, 2023
1feea0f
Monitoring script support for VQSR Lite WDL JointVcfFiltering.wdl
mcovarr Jun 13, 2023
fdc09c7
run test with dummy monitoring script
mcovarr Jun 21, 2023
e7edf9e
Move rather than delete GVS BigQuery classes
mcovarr Jun 23, 2023
dc44285
Process Sample gVCF headers during Ingest [VS-836]
mcovarr Jun 23, 2023
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run test with dummy monitoring script
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@mcovarr
mcovarr committed Jun 26, 2023
commit fdc09c72f5ac148a4509cc1ec60b7795605b5982
7 changes: 7 additions & 0 deletions scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh
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Expand Up @@ -32,6 +32,13 @@ sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" $CROMWELL_TEST_D

echo "Running Filtering WDL through cromwell"

cat > ${WORKING_DIR}/src/test/resources/cromwell_monitoring_script.sh <<FIN
while true
do
echo 'dummy monitoring script running...'
sleep 10
done
FIN
cat $WORKING_DIR/vcf_site_level_filtering_mod.json
java -jar $CROMWELL_JAR run $WDL_DIR/JointVcfFiltering.wdl -i $WORKING_DIR/vcf_site_level_filtering_mod.json

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5 changes: 3 additions & 2 deletions scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering.json
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Expand Up @@ -13,5 +13,6 @@
"JointVcfFiltering.annotations": ["ReadPosRankSum", "FS", "SOR", "QD"],
"JointVcfFiltering.output_prefix": "test_10_samples",
"JointVcfFiltering.resource_args": "--resource:hapmap,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz --resource:omni,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz --resource:1000G,training=true gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz --resource:mills,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointVcfFiltering.extract_extra_args": "-L chr21"
}
"JointVcfFiltering.extract_extra_args": "-L chr21",
"JointVcfFiltering.monitoring_script": "/home/runner/work/gatk/gatk/src/test/resources/cromwell_monitoring_script.sh"
}