Merge branch 'develop' into 132-fractional

Author: vsmalladi

.github/workflows/build.yml

@@ -25,6 +25,5 @@ jobs:
         uses: JamesIves/github-pages-deploy-action@v4
         with:
           branch: gh-pages
+          clean: true  # Clean only if on the main branch
           folder: .
-          target-folder: ${{ github.ref == 'refs/heads/main' && 'docs/index.html' || '' }}  # Deploy to docs/index.html only if on main
-          clean: ${{ github.ref == 'refs/heads/main' }}  # Clean only if on the main branch

.github/workflows/ci.yml

@@ -1,6 +1,7 @@
 name: Lint and validate OpenAPI specs
 on:
-  - pull_request
+  - push
+  - pull_request_target
 jobs:
   lint:
     name: Lint OpenAPI definition
@@ -12,10 +13,22 @@ jobs:
         uses: mhiew/redoc-lint-github-action@v4
         with:
           args: 'openapi/task_execution_service.openapi.yaml'
+  validate:
+    name: Validate OpenAPI definition
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out head branch
+        uses: actions/checkout@v4
+      - name: Run OpenAPI Validate Action
+        uses: swaggerexpert/swagger-editor-validate@v1
+        with:
+          definition-file: openapi/task_execution_service.openapi.yaml
+
   diff:
     name: Show OpenAPI differences relative to target branch
     runs-on: ubuntu-latest
-    if: ${{ github.event_name == 'pull_request' }}
+    outputs:
+      diff_generated: ${{ steps.upload-log.outputs.artifact_id }}
     steps:
       - name: Check out head branch
         uses: actions/checkout@v4
@@ -27,19 +40,39 @@ jobs:
         with:
           ref: ${{ github.event.pull_request.base.ref }}
           path: base
-      - name: Run OpenAPI Diff Action
-        uses: mvegter/openapi-diff-action@v0.23.5
+      - name: Create output directory
+        run: mkdir -p diff-artifacts/
+      - name: Pull Docker Image
+        run: docker pull openapitools/openapi-diff:2.0.1
+      - name: Run openapi-diff tool
+        run: |
+          docker run --rm \
+          -v $(pwd)/head:/head:ro \
+          -v $(pwd)/base:/base:ro \
+          -v $(pwd)/diff-artifacts:/local \
+          openapitools/openapi-diff:2.0.1 \
+          /base/openapi/task_execution_service.openapi.yaml \
+          /head/openapi/task_execution_service.openapi.yaml \
+          --markdown /local/diff.md 2> diff-artifacts/error.log
+      - name: Get PR number
+        id: get-pr-number
+        run: |
+          echo "${{ github.event.pull_request.number }}" > diff-artifacts/pr_number
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
         with:
-          head-spec: head/openapi/task_execution_service.openapi.yaml
-          base-spec: base/openapi/task_execution_service.openapi.yaml
+          name: diff-artifacts
+          path: diff-artifacts/
+          if-no-files-found: ignore
+      - name: Check if OpenAPI Diff failed
+        id: check-diff
+        run: |
+          if [ -s diff-artifacts/error.log  ]; then
+            echo "The diff failed. Please see artifact error.log."
+            exit 1
+          fi
 
-  validate:
-    name: Validate OpenAPI definition
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out head branch
-        uses: actions/checkout@v4
-      - name: Run OpenAPI Validate Action
-        uses: char0n/swagger-editor-validate@v1
-        with:
-          definition-file: openapi/task_execution_service.openapi.yaml
+permissions:
+  contents: read
+  pull-requests: write
+  issues: write

README.md

@@ -12,7 +12,7 @@ Task Execution Service (TES) API
 ================================
 
 This repository is the home for the schema of the Task Execution Service (TES)
-API defined by the[Cloud Work Stream](https://www.ga4gh.org/work_stream/cloud/)
+API defined by the [Cloud Work Stream](https://www.ga4gh.org/work_stream/cloud/)
 of the [Global Alliance for Genomics and Health (GA4GH)](https://ga4gh.org/).
 The goal of the API standard is to provide a uniform way to executing batch
 computing tasks.
@@ -92,11 +92,11 @@ handling personal data.
 > performed on latest versions of implementations available in December 2020.
 > Information may be outdated.
 
-|               | cwl-tes       | Cromwell  | Nextflow |
-| -----------   | ------------- | --------- | ---------|
-| **Funnel**    | [Compatible](https://github.com/ohsu-comp-bio/cwl-tes) | Compatible | [Compatible](https://www.nextflow.io/docs/latest/executor.html#ga4gh-tes) |
-| **TESK**      | [Compatible](https://github.com/ohsu-comp-bio/cwl-tes/pull/25) | [Compatible](https://cromwell.readthedocs.io/en/stable/backends/TES/) | [Compatible](https://github.com/EMBL-EBI-TSI/tesk-core/pull/19) |
-| **TES Azure** | Not tested | [Compatible](https://github.com/microsoft/CromwellOnAzure) | [Compatible](https://www.nextflow.io/docs/stable/executor.html#ga4gh-tes) |
+|               | cwl-tes       | Cromwell  | Nextflow | Snakemake |
+| -----------   | ------------- | --------- | ---------| --------- |
+| **Funnel**    | [Compatible](https://github.com/ohsu-comp-bio/cwl-tes) | Compatible | [Compatible](https://www.nextflow.io/docs/latest/executor.html#ga4gh-tes) | [Compatible](https://snakemake.readthedocs.io/en/stable/executing/cloud.html#executing-a-snakemake-workflow-via-ga4gh-tes) |
+| **TESK**      | [Compatible](https://github.com/ohsu-comp-bio/cwl-tes/pull/25) | [Compatible](https://cromwell.readthedocs.io/en/stable/backends/TES/) | [Compatible](https://github.com/EMBL-EBI-TSI/tesk-core/pull/19) | [Compatible](https://github.com/EMBL-EBI-TSI/tesk-core/pull/19) | [Compatible](https://github.com/elixir-cloud-aai/demo-tes-hybrid-cloud/tree/main) |
+| **TES Azure** | Not tested | [Compatible](https://github.com/microsoft/CromwellOnAzure) | [Compatible](https://www.nextflow.io/docs/stable/executor.html#ga4gh-tes) | [Compatible](https://github.com/microsoft/ga4gh-tes/blob/main/snakemake/examples/snakemake/README.md) |
 
 
 TES Service Examples