run test with dummy monitoring script

broadinstitute · Jun 23, 2023 · 23b750d · 23b750d
1 parent da32a71
commit 23b750d
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Showing 2 changed files with 10 additions and 2 deletions.
diff --git a/scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh b/scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh
@@ -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
 

diff --git a/scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering.json b/scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering.json
@@ -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"
+}