Merge branch 'main' into kj_issue_759_integrategq

broadinstitute · Jan 6, 2025 · d1b313b · d1b313b
2 parents 6632605 + a1f302d
commit d1b313b
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl b/inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/EvidenceQC.json.tmpl
@@ -8,10 +8,8 @@
   "EvidenceQC.genome_file": "${workspace.genome_file}",
 
   "EvidenceQC.batch": "${this.sample_set_id}",
-  "EvidenceQC.melt_insert_size": "${this.samples.melt_insert_size}",
   "EvidenceQC.counts": "${this.samples.coverage_counts}",
   "EvidenceQC.manta_vcfs": "${this.samples.manta_vcf}",
-  "EvidenceQC.melt_vcfs": "${this.samples.melt_vcf}",
   "EvidenceQC.wham_vcfs": "${this.samples.wham_vcf}",
   "EvidenceQC.scramble_vcfs": "${this.samples.scramble_vcf}",
   "EvidenceQC.samples": "${this.samples.sample_id}"

diff --git a/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl b/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl
@@ -10,7 +10,7 @@
   "EvidenceQC.batch": {{ test_batch.name | tojson }},
   "EvidenceQC.counts": {{ test_batch.counts | tojson }},
   "EvidenceQC.manta_vcfs": {{ test_batch.manta_vcfs | tojson }},
-  "EvidenceQC.melt_vcfs": {{ test_batch.melt_vcfs | tojson }},
   "EvidenceQC.wham_vcfs": {{ test_batch.wham_vcfs | tojson }},
+  "EvidenceQC.scramble_vcfs": {{ test_batch.scramble_vcf | tojson }},
   "EvidenceQC.samples": {{ test_batch.samples | tojson }}
 }
diff --git a/inputs/values/resources_hg38.json b/inputs/values/resources_hg38.json
@@ -17,9 +17,9 @@
   "depth_exclude_list_index" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/depth_blacklist.sorted.bed.gz.tbi",
   "empty_file" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/empty.file",
   "exclude_intervals_for_gcnv_filter_intervals" : "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/hg38.wgs.blacklist.wPAR.bed",
-  "external_af_population" : ["ALL", "AFR", "AMR", "EAS", "EUR"],
-  "external_af_ref_bed" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gnomad_AF/gnomad_v2.1_sv.sites.GRCh38.bed.gz",
-  "external_af_ref_bed_prefix" : "gnomad_v2.1_sv",
+  "external_af_population" : ["ALL", "AFR", "AMR", "EAS", "EUR", "MID", "FIN", "ASJ", "RMI", "SAS", "AMI"],
+  "external_af_ref_bed" : "gs://gatk-sv-resources-public/gnomad_AF/gnomad_v4_SV.Freq.tsv.gz",
+  "external_af_ref_bed_prefix" : "gnomad_v4.1_sv",
   "genome_file" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.genome",
   "hervk_reference": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/HERVK.sorted.bed.gz",
   "line1_reference": "gs://gatk-sv-resources-public/hg38/v0/sv-resources/resources/v1/LINE1.sorted.bed.gz",