yttria-aniseia · yttria-aniseia · Sep 9, 2025 · Dec 10, 2024 · Feb 12, 2025 · Feb 19, 2025
diff --git a/.dockstore.yml b/.dockstore.yml
@@ -1,20 +1,6 @@
 version: 1.2
 
 workflows:
-  - name: HiFi-human-WGS-WDL
-    subclass: WDL
-    primaryDescriptorPath: /workflows/main.wdl
-    readMePath: /README.md
-    authors:
-      - orcid: 0000-0001-5921-2022 # Juniper Lake
-      - orcid: 0000-0001-7628-5645 # Gregory Concepcion
-      - orcid: 0000-0003-1183-0432 # Aaron Wenger
-      - orcid: 0000-0002-7422-1194 # William Rowell
-      - orcid: 0000-0002-5507-0896 # Heather Ward
-      - orcid: 0009-0001-0205-4614 # Karen Fang
-    latestTagAsDefault: False
-    filters:
-      tags: [ /v1\..*dockstore/ ]
   - name: HiFi-human-WGS-WDL-singleton
     subclass: WDL
     primaryDescriptorPath: /workflows/singleton.wdl

diff --git a/.gitignore b/.gitignore
@@ -10,4 +10,6 @@ tests
 miniwdl_singularity_cache
 miniwdl_download_cache
 miniwdl_call_cache
-miniwdl_test_output
+miniwdl_test_output
+
+.venv
diff --git a/GRCh38.ref_map.v2p0p0.template.tsv b/GRCh38.ref_map.v2p0p0.template.tsv
diff --git a/GRCh38.ref_map.v3p0p0.template.tsv b/GRCh38.ref_map.v3p0p0.template.tsv
@@ -0,0 +1,10 @@
+name	GRCh38
+fasta	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
+fasta_index	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
+trgt_tandem_repeat_bed	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/trgt/adotto_strchive_20250626.hg38.bed.gz
+sawfish_exclude_bed	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz
+sawfish_exclude_bed_index	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz.tbi
+sawfish_expected_bed_male	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XY.bed
+sawfish_expected_bed_female	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XX.bed
+pharmcat_positions_vcf	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz
+pharmcat_positions_vcf_index	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz.csi
diff --git a/GRCh38.tertiary_map.v2p0p0.template.tsv b/GRCh38.tertiary_map.v2p0p0.template.tsv
diff --git a/GRCh38.tertiary_map.v3p0p0.template.tsv b/GRCh38.tertiary_map.v3p0p0.template.tsv
@@ -0,0 +1,12 @@
+slivar_js	<prefix>/hifi-wdl-resources-v3.0.0/slivar/slivar-functions.v0.2.8.js
+ensembl_gff	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
+lof_lookup	<prefix>/hifi-wdl-resources-v3.0.0/slivar/lof.gnomadv4p1.lookup
+clinvar_lookup	<prefix>/hifi-wdl-resources-v3.0.0/slivar/clinvar_gene_desc.20250618T144412.txt
+slivar_gnotate_files	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.2.0.deepvariant.glnexus.zip
+slivar_gnotate_prefixes	gnomad,colors
+slivar_max_af	0.03
+slivar_max_nhomalt	4
+slivar_max_ac	4
+slivar_min_gq	5
+svpack_pop_vcfs	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz
+svpack_pop_vcf_indices	<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,<prefix>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz.tbi
diff --git a/README.md b/README.md
@@ -24,18 +24,18 @@ Both workflows are designed to analyze human PacBio whole genome sequencing (WGS
 
 This is an actively developed workflow with multiple versioned releases, and we make use of git submodules for common tasks that are shared by multiple workflows. There are two ways to ensure you are using a supported release of the workflow and ensure that the submodules are correctly initialized:
 
-1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.1.2):
+1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v3.0.2):
 
   ```bash
-  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.2/hifi-human-wgs-singleton.zip
-  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.2/hifi-human-wgs-family.zip
+  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v3.0.2/hifi-human-wgs-singleton.zip
+  wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v3.0.2/hifi-human-wgs-family.zip
   ```
 
 2) Clone the repository and initialize the submodules:
 
   ```bash
   git clone \
-    --depth 1 --branch v2.1.2 \
+    --depth 1 --branch v3.0.2 \
     --recursive \
     https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git
   ```
@@ -127,7 +127,7 @@ At a high level, we have two types of inputs files:
 
 The resource bundle containing the GRCh38 reference and other files used in this workflow can be downloaded from Zenodo:
 
-[<img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14027047.svg" alt="10.5281/zenodo.14027047">](https://zenodo.org/records/14027047)
+[<img src="https://zenodo.org/badge/DOI/10.5281/zenodo.15750792.svg" alt="10.5281/zenodo.15750792">](https://zenodo.org/records/15750792)
 
 # Tool versions and Docker images
 

diff --git a/backends/aws-healthomics/GRCh38.ref_map.v2p0p0.aws.tsv b/backends/aws-healthomics/GRCh38.ref_map.v2p0p0.aws.tsv
diff --git a/backends/aws-healthomics/GRCh38.ref_map.v3p0p0.aws.tsv b/backends/aws-healthomics/GRCh38.ref_map.v3p0p0.aws.tsv
@@ -0,0 +1,10 @@
+name	GRCh38
+fasta	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
+fasta_index	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
+trgt_tandem_repeat_bed	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/trgt/adotto_strchive_20250626.hg38.bed.gz
+sawfish_exclude_bed	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz
+sawfish_exclude_bed_index	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz.tbi
+sawfish_expected_bed_male	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XY.bed
+sawfish_expected_bed_female	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XX.bed
+pharmcat_positions_vcf	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz
+pharmcat_positions_vcf_index	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz.csi
diff --git a/backends/aws-healthomics/GRCh38.tertiary_map.v2p0p0.aws.tsv b/backends/aws-healthomics/GRCh38.tertiary_map.v2p0p0.aws.tsv
diff --git a/backends/aws-healthomics/GRCh38.tertiary_map.v3p0p0.aws.tsv b/backends/aws-healthomics/GRCh38.tertiary_map.v3p0p0.aws.tsv
@@ -0,0 +1,12 @@
+slivar_js	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/slivar/slivar-functions.v0.2.8.js
+ensembl_gff	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
+lof_lookup	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/slivar/lof.gnomadv4p1.lookup
+clinvar_lookup	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/slivar/clinvar_gene_desc.20250618T144412.txt
+slivar_gnotate_files	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.2.0.deepvariant.glnexus.zip
+slivar_gnotate_prefixes	gnomad,colors
+slivar_max_af	0.03
+slivar_max_nhomalt	4
+slivar_max_ac	4
+slivar_min_gq	5
+svpack_pop_vcfs	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz
+svpack_pop_vcf_indices	s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,s3://<bucket_path>/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz.tbi
diff --git a/backends/aws-healthomics/family.healthomics.inputs.json b/backends/aws-healthomics/family.healthomics.inputs.json
@@ -15,8 +15,8 @@
     ]
   },
   "humanwgs_family.phenotypes": "String? (optional)",
-  "humanwgs_family.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v2p0p0.aws.tsv",
-  "humanwgs_family.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2p0p0.aws.tsv",
+  "humanwgs_family.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v3p0p0.aws.tsv",
+  "humanwgs_family.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v3p0p0.aws.tsv",
   "humanwgs_family.backend": "AWS-HealthOmics",
   "humanwgs_family.container_registry": "String",
   "humanwgs_family.preemptible": true

diff --git a/backends/aws-healthomics/singleton.healthomics.inputs.json b/backends/aws-healthomics/singleton.healthomics.inputs.json
@@ -5,8 +5,8 @@
     "File"
   ],
   "humanwgs_singleton.phenotypes": "String? (optional)",
-  "humanwgs_singleton.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v2p0p0.aws.tsv",
-  "humanwgs_singleton.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v2p0p0.aws.tsv",
+  "humanwgs_singleton.ref_map_file": "s3://<bucket_path>/GRCh38.ref_map.v3p0p0.aws.tsv",
+  "humanwgs_singleton.tertiary_map_file": "s3://<bucket_path>/GRCh38.tertiary_map.v3p0p0.aws.tsv",
   "humanwgs_singleton.backend": "AWS-HealthOmics",
   "humanwgs_singleton.container_registry": "String",
   "humanwgs_singleton.preemptible": true

diff --git a/backends/azure/GRCh38.ref_map.v2p0p0.azure.tsv b/backends/azure/GRCh38.ref_map.v2p0p0.azure.tsv
diff --git a/backends/azure/GRCh38.ref_map.v3p0p0.azure.tsv b/backends/azure/GRCh38.ref_map.v3p0p0.azure.tsv
@@ -0,0 +1,10 @@
+name	GRCh38
+fasta	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
+fasta_index	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
+trgt_tandem_repeat_bed	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/trgt/adotto_strchive_20250626.hg38.bed.gz
+sawfish_exclude_bed	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz
+sawfish_exclude_bed_index	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/annotation_and_common_cnv.hg38.bed.gz.tbi
+sawfish_expected_bed_male	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XY.bed
+sawfish_expected_bed_female	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sawfish/expected_cn.hg38.XX.bed
+pharmcat_positions_vcf	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz
+pharmcat_positions_vcf_index	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz.csi
diff --git a/backends/azure/GRCh38.tertiary_map.v2p0p0.azure.tsv b/backends/azure/GRCh38.tertiary_map.v2p0p0.azure.tsv
diff --git a/backends/azure/GRCh38.tertiary_map.v3p0p0.azure.tsv b/backends/azure/GRCh38.tertiary_map.v3p0p0.azure.tsv
@@ -0,0 +1,12 @@
+slivar_js	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/slivar/slivar-functions.v0.2.8.js
+ensembl_gff	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
+lof_lookup	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/slivar/lof.gnomadv4p1.lookup
+clinvar_lookup	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/slivar/clinvar_gene_desc.20250618T144412.txt
+slivar_gnotate_files	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.2.0.deepvariant.glnexus.zip
+slivar_gnotate_prefixes	gnomad,colors
+slivar_max_af	0.03
+slivar_max_nhomalt	4
+slivar_max_ac	4
+slivar_min_gq	5
+svpack_pop_vcfs	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz
+svpack_pop_vcf_indices	https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,https://datasetpbrarediseases.blob.core.windows.net/dataset/hifi-wdl-resources-v3.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.2.0.pbsv.jasmine.vcf.gz.tbi