From 5b61044476b04d07224329f7a1128896dd0fcdd3 Mon Sep 17 00:00:00 2001 From: Megan Shand Date: Thu, 22 Sep 2022 09:04:50 -0400 Subject: [PATCH] addressing comments --- .../vcf_site_level_filtering_travis.json | 3 ++- scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl | 5 +++-- 2 files changed, 5 insertions(+), 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 index 2823cdc865c..8bae8c7f5a2 100644 --- 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 } \ No newline at end of file diff --git a/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl b/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl index 11ef35a614b..4ec1f1a3887 100644 --- 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