test monitoring script

broadinstitute · Jun 21, 2023 · 585d0c8 · 585d0c8
1 parent eeea9a2
commit 585d0c8
Showing 1 changed file with 3 additions and 2 deletions.
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"
+}