addressing comments

broadinstitute · Sep 22, 2022 · 5b61044 · 5b61044
1 parent 718cda4
commit 5b61044
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering_travis.json b/scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering_travis.json
@@ -9,5 +9,6 @@
   "JointVcfFiltering.basename": "test_10_samples",
   "JointVcfFiltering.snp_annotations": "-A ReadPosRankSum -A FS -A SOR -A QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
   "JointVcfFiltering.indel_annotations": "-A MQRankSum -A ReadPosRankSum -A FS -A SOR -A QD -A AVERAGE_TREE_SCORE",
-  "JointVcfFiltering.model_backend": "PYTHON_IFOREST"
+  "JointVcfFiltering.model_backend": "PYTHON_IFOREST",
+  "JointVcfFiltering.use_allele_specific_annotations": false
 }
diff --git a/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl b/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl
@@ -27,7 +27,7 @@ workflow JointVcfFiltering {
 		String indel_annotations
 		File? gatk_override
 
-		Boolean use_allele_specific_annotations = false
+		Boolean use_allele_specific_annotations
 
 		String snp_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,calibration=false gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
 		String indel_resource_args = "--resource:mills,training=true,calibration=true gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
@@ -271,7 +271,8 @@ task ScoreVariantAnnotations {
 				--resource:extracted,extracted=true ~{extracted_training_vcf} \
 				~{resource_args}
 		else
-			echo "Input VCF was empty so we'll return the same VCF that was input"
+			echo "Input VCF was empty so we'll return the same VCF that was input."
+			echo "Scores and annot hdf5 files will not be produced since the input was empty."
 			ln -s ~{vcf} ~{basename}.~{mode}.vcf.gz
 			ln -s ~{vcf_index} ~{basename}.~{mode}.vcf.gz.tbi
 		fi