Update Nextflow and Compliance Tests

.github/workflows/compliance-test.yaml

@@ -1,23 +1,18 @@
 # Workflow for running the TES compliance suite against Funnel
-
+#
 # This includes the following steps:
 #  1. Build Funnel and store the resulting binary artifact
 #  2. Install tes-compliance-suite and run against every version of TES simultaneously
 #  3. start-report-deployment: Send a dispatch to the funnel-compliance repository to generate and publish
 #     the tes-compliance-suite report to https://ohsu-comp-bio.github.io/funnel-compliance/
-
+#
 # Optionally debug via SSH
 # Ref: https://fleetdm.com/engineering/tips-for-github-actions-usability
 #
 # To use this step uncomment and place anywhere in the build steps. The build will pause on this step and
 # output a ssh address associated with the Github action worker. Helpful for debugging build steps and
 # and intermediary files/artifacts.
 #
-# - name: "Debug: Package dependancies for tmate (CentOS)"
-#   run: |
-#     yum install -y xz
-#     ln -s /bin/true /bin/apt-get
-#
 # - name: Setup tmate session
 #   uses: mxschmitt/action-tmate@v3
 
@@ -29,10 +24,9 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: quay.io/ohsu-comp-bio/slurm
     steps:
     - name: Set up Go 1.x
-      uses: actions/setup-go@v2
+      uses: actions/setup-go@v5
       with:
         go-version: 1.21
 
@@ -54,19 +48,16 @@ jobs:
       matrix:
         version: [1.0.0, 1.1.0]
         db: ["boltdb", "mongodb"]
-        compute: ["local", "slurm"]
+        compute: ["local"]
     needs: build
     runs-on: ubuntu-latest
-    container:
-      image: quay.io/ohsu-comp-bio/slurm
-      options: --hostname slurmctl --cap-add sys_admin
     steps:
       # Required to access the 'tests/mongo.config.yml' file
       # Perhaps uploading it as an artifact would be more efficient?
       - name: Check out code
         uses: actions/checkout@v2
 
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v3
         with:
           name: funnelBin
 
@@ -76,60 +67,17 @@ jobs:
           if [ ${{ matrix.db }} = "mongodb" ]; then
             make start-mongodb
             cat `pwd`/tests/mongo.config.yml >> config.yml
-            # Required for Funnel to connect MongoDB
-            echo "172.17.0.1 localhost" >> /etc/hosts
-          elif [ ${{ matrix.compute }} = "slurm" ]; then
-            cat `pwd`/tests/slurm.config.yml >> config.yml
-            cp config.yml /opt/funnel_config.yml
-            # Start Slurm
-            /usr/local/bin/docker-entrypoint.sh
           fi
           chmod +x funnel
-          FLAGS="--config `pwd`/config.yml"
-          ./funnel server run $FLAGS &> funnel.logs &
+          ./funnel server run --config `pwd`/config.yml &> funnel.logs &
 
       - name: Run OpenAPI Test Runner
         run: |
-          # Clone the 'upstream' OpenAPI Test Runner when PR #65 is merged
-          # https://github.com/elixir-cloud-aai/openapi-test-runner/pull/65
-          # git clone https://github.com/elixir-cloud-aai/openapi-test-runner
-          git clone https://github.com/ohsu-comp-bio/openapi-test-runner -b fix/create-and-filter-task
-          
+          git clone https://github.com/elixir-cloud-aai/openapi-test-runner
           cd openapi-test-runner
           python3 -m venv venv
           source venv/bin/activate
           pip install -r requirements.txt
           python setup.py install  
           openapi-test-runner report --version "${{ matrix.version }}" --server "http://localhost:8000/"
 
-      - name: Install TES compliance suite
-        run: |
-          git clone https://github.com/lbeckman314/tes-compliance-suite -b feature/tesv1.1
-          cd tes-compliance-suite
-          /root/.pyenv/shims/python3 -m venv venv
-          source venv/bin/activate
-          pip install -r requirements.txt
-          python setup.py install
-          mkdir reports
-
-      - name: Test compliance (Report Publishing)
-        run: |
-          cd tes-compliance-suite
-          source venv/bin/activate
-          tes-compliance-suite report --version "${{ matrix.version }}" --server "http://localhost:8000/"
-
-  start-report-deployment:
-    needs: compliance
-    runs-on: ubuntu-latest
-    steps:
-      # https://docs.github.com/en/rest/repos/repos?apiVersion=2022-11-28#create-a-repository-dispatch-event
-      - name: Start report generation
-        uses: passeidireto/trigger-external-workflow-action@main
-        env:
-          PAYLOAD_AUTHOR: "Funnel"
-          PAYLOAD_REVISION: "3"
-        with:
-          repository: ohsu-comp-bio/funnel-compliance
-          event: start-report
-          github_pat: ${{ secrets.ACTIONS_TOKEN }}
-

.github/workflows/nextflow.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Set up Go 1.x
-      uses: actions/setup-go@v2
+      uses: actions/setup-go@v5
       with:
         go-version: 1.21
 
@@ -29,28 +29,25 @@ jobs:
     needs: build
     steps:
     - name: Download Funnel
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@v2
       with:
         name: funnelBin
         path: funnel
 
     - name: Start Funnel
-      working-directory: 
       run: |
         cd funnel/
         chmod +x ./funnel
         ./funnel server --LocalStorage.AllowedDirs $HOME run &
 
     - name: Install Nextflow
       run: |
-        cd ..
-        git clone https://github.com/nextflow-io/nextflow/ -b tes-update-1.1
+        git clone https://github.com/nextflow-io/nextflow
         cd nextflow
         make compile
 
     - name: Install nf-canary and GA4GH-TES plugin
       run: |
-        cd ..
         git clone https://github.com/seqeralabs/nf-canary
         cd nf-canary
         cat <<EOF >> nextflow.config
@@ -60,8 +57,8 @@ jobs:
           process.executor = 'tes'
           tes.endpoint = 'http://localhost:8000'
         EOF
-  
+
     - name: Run nf-canary tests
       run: |
-        cd ../nf-canary
-        ../nextflow/launch.sh run main.nf
+        ./nextflow/nextflow run nf-canary/main.nf
+