Merge pull request #136 from PacificBiosciences/feature/v2

v2 release

.dockstore.yml

@@ -1,69 +1,47 @@
-# The first line refers to the version 1.2 of the .dockstore.yml schema
 version: 1.2
 
-# An array of workflows. Each element corresponds to a workflow on Dockstore.
 workflows:
-
-  # The optional workflow name for a workflow, which may only consist of alphanumerics
-  # and internal underscores and hyphens, but no spaces or other characters. Names may not exceed 256 characters.
-  # If using a .dockstore.yml with multiple workflows, this field is required
-  # to uniquely identify workflows in the repository.
-  #
-  # It should be noted that having the name come first is an arbitrary decision.
-  # You could use subclass instead, for instance. Provided arrays are not broken
-  # up, the order of fields within a .dockstore.yml is not important.
   - name: HiFi-human-WGS-WDL
-
-    # The descriptor language used for the workflow. CWL, WDL, NFL (Nextflow), or GALAXY.
-    # This cannot be changed once the workflow is registered.
     subclass: WDL
-
-    # Workflow-wide setting that will affect ALL branches/tags; only set this as needed in a main branch.
-    # Set to true to publish an unpublished workflow, or false to unpublish a published workflow.
-    # Omitting the publish setting leaves the publish-state unchanged (recommended for all non-primary branches).
-    # publish: <Boolean>
-
-    # The absolute path to the primary descriptor file in the Git repository.
-    # - For CWL, the primary descriptor is a .cwl file.
-    # - For WDL, the primary descriptor is a .wdl file.
-    # - For Galaxy, the primary descriptor is a .ga file.
-    # - Nextflow differs from these as the primary descriptor is a nextflow.config file.
     primaryDescriptorPath: /workflows/main.wdl
-
-    # An optional array of absolute paths to test parameter files in the Git repository.
-    # For example...
-    # testParameterFiles:
-    #   - /null-model/null-model.json
-    #   - /null-model/null-model-binary.json
-    # testParameterFiles: <String Array>
-
-    # An optional path to a workflow-specific readme in the Git repository. If not provided, Dockstore will show
-    # the readme.md present at the root of the Git repository if it is present.
-    # If you have multiple workflows in a single Git repository, it is recommend to give each one a readme.
     readMePath: /README.md
-
-    # An optional array of authorship information.
-    # Note that if orcid is present, then all other fields will be ignored, as information will be taken from orcid.
-    # If orcid is not present, make sure to at a minimum include the name field for each author.
     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
-
-    # A boolean that will change the default version to be displayed on Dockstore. Default: False.
-    # A value of true will automatically display the latest tag updated as default.
-    # A value of false will retain the default version that has been specified via the Dockstore UI.
     latestTagAsDefault: False
-
-    # The optional filters section allow specifying sets of Git branches and tags to include for the workflow.
-    # If no filters are given, all branches and tags are included.
-    # Branches and tags are arrays of pattern-strings.
-    # Pattern-strings use Unix-style Glob syntax by default (Ex: `develop`, `myworkflow/**`)
-    # https://docs.oracle.com/en/java/javase/11/docs/api/java.base/java/nio/file/FileSystem.html#getPathMatcher(java.lang.String)
-    # or RegEx when the string is surrounded by / (Ex: `/develop/`, `/myworkflow\/.*/`).
+    filters:
+      tags: [ /v1\..*dockstore/ ]
+  - name: HiFi-human-WGS-WDL-singleton
+    subclass: WDL
+    primaryDescriptorPath: /workflows/singleton.wdl
+    readMePath: /docs/singleton.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:
+      branches: [ /.*dockstore/ ]
+      tags: [ /v.*dockstore/ ]
+  - name: HiFi-human-WGS-WDL-family
+    subclass: WDL
+    primaryDescriptorPath: /workflows/family.wdl
+    readMePath: /docs/family.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:
       branches: [ /.*dockstore/ ]
-      tags: [ /v.*/ ]
+      tags: [ /v.*dockstore/ ]

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "workflows/wdl-common"]
 	path = workflows/wdl-common
-	url = https://github.com/PacificBiosciences/wdl-common
+	url = ../wdl-common.git

GRCh38.ref_map.v2p0p0.template.tsv

@@ -0,0 +1,12 @@
+name	GRCh38
+fasta	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta
+fasta_index	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.fasta.fai
+pbsv_splits	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.pbsv_splits.json
+pbsv_tandem_repeat_bed	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/human_GRCh38_no_alt_analysis_set.trf.bed
+trgt_tandem_repeat_bed	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/trgt/human_GRCh38_no_alt_analysis_set.trgt.v0.3.4.bed
+hificnv_exclude_bed	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz
+hificnv_exclude_bed_index	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/cnv.excluded_regions.common_50.hg38.bed.gz.tbi
+hificnv_expected_bed_male	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XY.bed
+hificnv_expected_bed_female	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/hificnv/expected_cn.hg38.XX.bed
+pharmcat_positions_vcf	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz
+pharmcat_positions_vcf_index	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/pharmcat/pharmcat_positions_2.15.4.vcf.bgz.csi

GRCh38.tertiary_map.v2p0p0.template.tsv

@@ -0,0 +1,12 @@
+slivar_js	<prefix>/hifi-wdl-resources-v2.0.0/slivar/slivar-functions.v0.2.8.js
+ensembl_gff	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/ensembl.GRCh38.101.reformatted.gff3.gz
+lof_lookup	<prefix>/hifi-wdl-resources-v2.0.0/slivar/lof_lookup.v2.1.1.txt
+clinvar_lookup	<prefix>/hifi-wdl-resources-v2.0.0/slivar/clinvar_gene_desc.20240624T165443.txt
+slivar_gnotate_files	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/slivar_gnotate/gnomad.hg38.v4.1.custom.v1.zip,<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/slivar_gnotate/CoLoRSdb.GRCh38.v1.1.0.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-v2.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz,<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz
+svpack_pop_vcf_indices	<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/sv_pop_vcfs/gnomad.v4.1.sv.sites.pass.vcf.gz.tbi,<prefix>/hifi-wdl-resources-v2.0.0/GRCh38/sv_pop_vcfs/CoLoRSdb.GRCh38.v1.1.0.pbsv.jasmine.vcf.gz.tbi

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2023, Pacific Biosciences of California, Inc.
+Copyright (c) 2024, Pacific Biosciences of California, Inc.
 
 All rights reserved.