modules/.github/workflows/update-sentieon-snapshot.yml at 14ef8744d41b8322790f6c87c281b9e52de935e2 · nf-core/modules · GitHub

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name: update-sentieon-snapshot
run-name: update sentieon snapshot (automated)
on:
  issue_comment:
    types: [created]

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
  NFT_VER: "0.9.4"
  NXF_ANSI_LOG: false
  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
  NXF_VER: "25.10.2"

jobs:
  update-sentieon-snapshot:
    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
    if: >
      contains(github.event.comment.html_url, '/pull/') &&
      contains(github.event.comment.body, '@nf-core-bot update sentieon snapshot') &&
      github.repository == 'nf-core/modules'
    runs-on:
      - runs-on=${{ github.run_id }}-nf-test-changes
      - runner=4cpu-linux-x64
      - image=ubuntu22-full-x64
    steps:
      # indication that the snapshot is being updated
      - name: React on comment
        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: eyes
      # Use the @nf-core-bot token to check out so we can push later
      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        with:
          token: ${{ secrets.nf_core_bot_auth_token }}

      - name: Get the test path from the comment (after "@nf-core-bot update sentieon snapshot path:")
        id: get-test-path
        run: |
          echo "test_path=$(echo ${{ github.event.comment.body }} | grep -oP 'path:\s*\K[^ ]+')" >> $GITHUB_OUTPUT

      - name: if test path is empty, exit
        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
        if: steps.get-test-path.outputs.test_path == ''
        with:
          comment-id: ${{ github.event.comment.id }}
          reactions: "-1"

      - name: if test path is empty, exit
        if: steps.get-test-path.outputs.test_path == ''
        run: exit 0

      # Action runs on the issue comment, so we don't get the PR by default
      # Use the gh cli to check out the PR
      - name: Checkout Pull Request
        run: gh pr checkout ${{ github.event.issue.number }}
        env:
          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

      - uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5
        with:
          distribution: "temurin"
          java-version: "17"

      - name: Set up Nextflow
        uses: nf-core/setup-nextflow@v2
        with:
          version: "${{ env.NXF_VER }}"

      - name: Set up Python
        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
        with:
          python-version: "3.14"

      - name: Set up nf-test
        uses: nf-core/setup-nf-test@v1
        with:
          version: "${{ env.NFT_VER }}"
          install-pdiff: true

      # Set up secrets
      - name: Set up Nextflow secrets
        env:
          SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
          SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
        if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
        shell: bash
        run: |
          python -m pip install cryptography
          nextflow secrets set SENTIEON_AUTH_DATA $(python3 modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
      - name: Update sentieon snapshot
        id: update-sentieon-snapshot
        env:
          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
          SENTIEON_AUTH_MECH: "GitHub Actions - token"
        run: |
          nf-test test \
          --profile=docker \
          --verbose \
          --ci \
          --update-snapshot \
          --clean-snapshot \
          --filter process,workflow \
          --tag sentieon \
          ${{ steps.get-test-path.outputs.test_path }}

      - name: clean up
        run: |
          rm -rf setup-nextflow

      - name: Commit & push changes
        run: |
          git config user.email "core@nf-co.re"
          git config user.name "nf-core-bot"
          git config push.default upstream
          git add .
          git status
          git commit -m "[automated] Update sentieon snapshot"
          git push