Merge pull request #13 from PacificBiosciences/develop

Develop

.dockstore.yml

@@ -0,0 +1,68 @@
+# 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: wdl-humanassembly
+
+    # 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+    # Set to true to publish an unpublished workflow, or false to unpublish a published workflow.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: 0000-0002-7422-1194 # 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:
+      branches: [ /(.*)?dockstore/ ]
+      tags: [ /v.*dockstore/ ]

.github/workflows/lint-test-workflows.yml

@@ -11,7 +11,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/wdl-ci@v0.1.6
+        uses: dnastack/wdl-ci@v1.0.0
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}

.gitignore

@@ -0,0 +1,3 @@
+inputs.test_data*.json
+.wdltest*
+dependencies.zip

LICENSE

@@ -0,0 +1,34 @@
+Copyright (c) 2023, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above
+   copyright notice, this list of conditions and the following
+   disclaimer in the documentation and/or other materials provided
+   with the distribution.
+
+ * Neither the name of Pacific Biosciences nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.