awsfulltest.yml

name: nf-core AWS full size tests
# This workflow is triggered on PRs opened against the master branch.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on AWS batch

on:
  pull_request:
    branches:
      - master
  workflow_dispatch:
  pull_request_review:
    types: [submitted]

jobs:
  run-platform:
    name: Run AWS full tests
    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
    if: github.repository == 'nf-core/viralrecon' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
    runs-on: ubuntu-latest
    # Do a full-scale run with data from each sequencing platform
    strategy:
      matrix:
        platform: ["illumina", "nanopore"]
    steps:
      - uses: octokit/request-action@v2.x
        id: check_approvals
        with:
          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      - id: test_variables
        if: github.event_name != 'workflow_dispatch'
        run: |
          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
      - name: Launch workflow via Seqera Platform
        uses: seqeralabs/action-tower-launch@v2
        with:
          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
          revision: ${{ github.sha }}
          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/viralrecon/work-${{ github.sha }}
          parameters: |
            {
              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralrecon/results-${{ github.sha }}/platform_${{ matrix.platform }}"
            }
          profiles: test_full_${{ matrix.platform }},aws_tower
      - uses: actions/upload-artifact@v4
        with:
          name: Seqera Platform debug log file
          path: |
            seqera_platform_action_*.log
            seqera_platform_action_*.json