From fde9e1c9b3cbdf4c0df86468453f68242e21032b Mon Sep 17 00:00:00 2001 From: knathamuni <144271815+knathamuni@users.noreply.github.com> Date: Thu, 19 Dec 2024 14:16:26 -0500 Subject: [PATCH 1/3] added gnomad v4 annotation file, prefix, and additional subpopulations (#757) --- inputs/values/resources_hg38.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/inputs/values/resources_hg38.json b/inputs/values/resources_hg38.json index 545d4b2b0..e8d86638f 100644 --- 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", From 0f37c11d51c34fc49c33f0e3845daf2ab8c66bd1 Mon Sep 17 00:00:00 2001 From: Vahid Date: Thu, 2 Jan 2025 12:33:54 -0500 Subject: [PATCH 2/3] Update EvidenceQC templates (#763) * Update EvidenceQC templates * Remove melt_vcfs. --- .../cohort_mode/workflow_configurations/EvidenceQC.json.tmpl | 2 -- inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl | 2 +- 2 files changed, 1 insertion(+), 3 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 index 273ccba36..654c926a9 100644 --- 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 index b3937d578..e79997b5b 100644 --- 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 }}, "EvidenceQC.samples": {{ test_batch.samples | tojson }} } From a1f302d95dc397d8aa72de7dac2b397ea8884a9d Mon Sep 17 00:00:00 2001 From: Vahid Date: Thu, 2 Jan 2025 13:41:40 -0500 Subject: [PATCH 3/3] Template bug fix (#764) --- inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl b/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl index e79997b5b..1785b00d1 100644 --- a/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl +++ b/inputs/templates/test/EvidenceQC/EvidenceQC.json.tmpl @@ -11,6 +11,6 @@ "EvidenceQC.counts": {{ test_batch.counts | tojson }}, "EvidenceQC.manta_vcfs": {{ test_batch.manta_vcfs | tojson }}, "EvidenceQC.wham_vcfs": {{ test_batch.wham_vcfs | tojson }}, - "EvidenceQC.scramble_vcfs": {{ test_batch.scramble_vcf }}, + "EvidenceQC.scramble_vcfs": {{ test_batch.scramble_vcf | tojson }}, "EvidenceQC.samples": {{ test_batch.samples | tojson }} }