add nextflow d30e48d

nextflow/.github/workflows/README.md

@@ -0,0 +1,15 @@
+# Action 
+
+## Syntax
+
+https://help.github.com/en/articles/workflow-syntax-for-github-actions
+https://help.github.com/en/articles/contexts-and-expression-syntax-for-github-actions
+https://help.github.com/en/articles/virtual-environments-for-github-actions#environment-variables
+https://help.github.com/en/articles/configuring-docker-for-use-with-github-package-registry
+https://help.github.com/en/articles/virtual-environments-for-github-actions#creating-and-using-secrets-encrypted-variables
+
+## Java 
+
+Java VMs has to match the ones at this link https://static.azul.com/zulu/bin 
+
+Check the name *-jdk(x.y.z)

nextflow/.github/workflows/build.yml

@@ -0,0 +1,296 @@
+name: Nextflow CI
+# read more here: https://help.github.com/en/articles/workflow-syntax-for-github-actions#on
+
+# Note: We don't use the `on: path` option for docs,
+# because the Build steps are *required* tests.
+# Instead, we trigger + skip the tests if the only changes
+# are in the docs folder. GitHub treats this as passing.
+
+on:
+  push:
+    branches:
+      - 'master'
+      - 'test*'
+      - 'dev*'
+      - 'STABLE-*'
+  pull_request:
+    types: [opened, reopened, synchronize]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    timeout-minutes: 100
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: [17, 25]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Get the commit message
+        id: get_commit_message
+        run: |
+            if [ "${{ github.event_name }}" = "pull_request" ]; then
+                echo "GitHub event=pull_request"
+                COMMIT_SHA="${{ github.event.pull_request.head.sha }}"
+                COMMIT_MESSAGE="$(curl -s \
+                  -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
+                  https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message' | head -n 1)"
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
+            else
+                echo "GitHub event=${{ github.event_name }}"
+                # Extract only the first line of the commit message
+                COMMIT_MESSAGE="$(git log -1 --pretty=format:'%s')"
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
+            fi
+
+      - name: Setup env
+        run: |
+             rm -f $HOME/.gitconfig;
+             mkdir -p "$HOME/.nextflow";
+             echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
+        env:
+          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
+
+      - name: Setup Java ${{ matrix.java_version }}
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{matrix.java_version}}
+          distribution: 'temurin'
+          architecture: x64
+          cache: gradle
+
+      - name: Compile
+        run: make assemble
+
+      - name: Test
+        run: |
+            env | sort
+            # configure test env
+            if [[ "$GOOGLE_SECRET" ]]; then
+            echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
+            export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
+            fi
+            # run tests
+            make test
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          AWS_S3FS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_S3FS_SECRET_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
+          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
+          NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
+          NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
+          GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
+          AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
+          AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
+          AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
+          AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
+
+      - name: Publish tests report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: report-unit-tests-jdk-${{ matrix.java_version }}
+          path: |
+            **/build/reports/tests/test
+
+    outputs:
+      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
+
+  test:
+    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') }}
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: [17, 25]
+        test_mode: ["test_integration", "test_parser_v2", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Setup env
+        run: |
+          rm -f $HOME/.gitconfig;
+          mkdir -p "$HOME/.nextflow";
+          echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
+        env:
+          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
+
+      - name: Setup Java ${{ matrix.java_version }}
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{matrix.java_version}}
+          distribution: 'temurin'
+          architecture: x64
+          cache: gradle
+
+      - name: Run tests
+        run: |
+          env | sort
+          # configure test env
+          if [[ "$GOOGLE_SECRET" ]]; then
+          echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
+          export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
+          fi
+          cat $HOME/.nextflow/scm
+          make clean assemble install
+          bash test-ci.sh
+        env:
+          TEST_JDK: ${{ matrix.java_version }}
+          TEST_MODE: ${{ matrix.test_mode }}
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+          TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          AWS_DEFAULT_REGION: eu-west-1
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
+          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
+          NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
+          NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
+          GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
+          AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
+          AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
+          AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
+          AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
+
+      - name: Tar integration tests
+        if: always()
+        run: | 
+            tar -cvf integration-tests.tar.gz tests/checks
+            tar -cvf validation-tests.tar.gz validation
+
+      - name: Publish tests report
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
+          path: |
+            validation-tests.tar.gz
+            integration-tests.tar.gz
+
+  test-e2e:
+      if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}
+      needs: build
+      runs-on: ubuntu-latest
+      timeout-minutes: 10
+      permissions:
+          actions: write  # Allow writing to actions
+          contents: write # Allow writing to repository contents
+      steps:
+          - name: Checkout
+            uses: actions/checkout@v4
+            with:
+                fetch-depth: 1
+                submodules: true
+                
+          - name: Setup Java 17
+            uses: actions/setup-java@v4
+            with:
+                java-version: 17
+                distribution: 'temurin'
+                architecture: x64
+                cache: gradle
+
+          - name: Setup env
+            run: |
+                wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64
+                chmod +x wave
+                mv wave /usr/local/bin/
+                echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV
+
+          - name : Docker Login to Seqera public CR
+            uses : docker/login-action@v3
+            with :
+                registry : "public.cr.seqera.io"
+                username : "public-cr-admin"
+                password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
+
+          - name: Launch tests
+            run: |
+                cd test-e2e
+                bash run.sh
+            env:
+                GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }}
+                GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+
+  release:
+    if: ${{ always() && contains(needs.build.outputs.commit_message, '[release]') && needs.build.result == 'success' && (needs.test.result == 'success' || needs.test.result == 'skipped') }}
+    needs: [build, test]
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      actions: write
+      contents: write
+      packages: write
+      pull-requests: write
+      issues: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          submodules: true
+
+      - name: Setup Java 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: 17
+          distribution: 'temurin'
+          architecture: x64
+          cache: gradle
+
+      - name: Configure Git
+        run: |
+          git config --global user.name "${{ github.event.pusher.name || github.actor }}"
+          git config --global user.email "${{ github.event.pusher.email || format('{0}@users.noreply.github.com', github.actor) }}"
+
+      - name: Docker Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Docker Login to Seqera public CR
+        uses: docker/login-action@v3
+        with:
+          registry: "public.cr.seqera.io"
+          username: ${{ vars.SEQERA_PUBLIC_CR_USERNAME }}
+          password: ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
+
+      - name: Run release
+        run: |
+          echo "Starting release process..."
+          echo "npr.apiUrl=$NPR_API_URL" >> gradle.properties
+          echo "npr.apiKey=$NPR_API_KEY" >> gradle.properties
+          bash release.sh
+        env:
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
+          AWS_JAVA_V1_DISABLE_DEPRECATION_ANNOUNCEMENT: 'true'
+          # credentials to pubslish nextflow assets
+          NXF_AWS_ACCESS: ${{ vars.NXF_AWS_ACCESS }}
+          NXF_AWS_SECRET: ${{ secrets.NXF_AWS_SECRET }}
+          # credentials to publish maven libraries
+          AWS_ACCESS_KEY_ID: ${{ vars.SEQERA_MAVEN_ACCESS_KEY }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.SEQERA_MAVEN_SECRET_KEY }}
+          # plugin registry
+          NPR_API_URL: ${{ vars.NPR_API_URL }}
+          NPR_API_KEY: ${{ secrets.NPR_API_KEY }}
+          # GitHub secrets
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

nextflow/.github/workflows/cffconvert.yml

@@ -0,0 +1,19 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v4
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/cffconvert-github-action@2.0.0
+        with:
+          args: "--validate"

nextflow/.github/workflows/claude.yml

@@ -0,0 +1,36 @@
+name: Claude PR Assistant
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude-code-action:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && contains(github.event.issue.body, '@claude'))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude PR Action
+        uses: anthropics/claude-code-action@beta
+        with:
+          anthropic_api_key: ${{ secrets.NEXTFLOW_ANTHROPIC_API_KEY }}
+          timeout_minutes: "60"

nextflow/.github/workflows/docs.yml

@@ -0,0 +1,22 @@
+name: Docs CI
+on:
+  pull_request:
+    types: [opened, reopened, synchronize]
+    paths:
+      - 'docs/**'
+  workflow_dispatch:
+jobs:
+  docs-build:
+    name: Build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Test docs build
+        run: |
+          cd docs/
+          pip install -r requirements.txt
+          make clean html

nextflow/.github/workflows/stale.yml

@@ -0,0 +1,21 @@
+name: 'Mark stale issues and PRs'
+on:
+  schedule:
+    - cron: '30 1 * * *'
+  workflow_dispatch:
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v9
+        with:
+          days-before-stale: 180
+          days-before-close: -1
+          stale-issue-label: stale
+          stale-issue-message: ''
+          stale-pr-label: stale
+          stale-pr-message: ''
+          exempt-issue-labels: bug,planned,security
+          exempt-all-milestones: true
+          exempt-all-assignees: true