cloudtest.yml

name: nf-core cloud test

on:
  release:
    types: [created]
  workflow_dispatch:
    inputs:
      test:
        description: "-profile test (smaller)"
        type: boolean
        default: true
      somatic:
        description: "Somatic full test"
        type: boolean
        default: false
      germline:
        description: "Germline full test"
        type: boolean
        default: false
      germline_ncbench_agilent:
        description: "Germline Agilent NCBench test"
        type: boolean
        default: false
      aws:
        description: "AWS Batch"
        type: boolean
        default: true
      azure:
        description: "Azure Batch"
        type: boolean
        default: true

jobs:
  trigger-profile-test:
    name: Run AWS tests
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        include:
          - profile: test_aws
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.aws ) ) }}
          - profile: test_azure
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.test && inputs.azure ) ) }}
          - profile: test_full_aws
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.aws ) ) }}
          - profile: test_full_azure
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.somatic && inputs.azure ) ) }}
          - profile: test_full_germline_aws
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }}
          - profile: test_full_germline_azure
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }}
          - profile: test_full_germline_ncbench_agilent_aws
            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }}

    steps:
      # Launch workflow on AWS Batch
      - name: AWS Launch
        uses: seqeralabs/action-tower-launch@v2
        if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.aws ) }}
        with:
          run_name: sarek_${{ matrix.profile }}
          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/sarek/work-${{ github.sha }}/${{ matrix.profile }}
          parameters: |
            {
              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
            }
          profiles: ${{ matrix.profile }}

      - uses: actions/upload-artifact@v3
        name: Save AWS Logs
        if: success() || failure()
        with:
          name: tower-aws-${{ matrix.profile }}-log
          path: |
            tower_action_*.log
            tower_action_*.json

      # Launch workflow using Tower CLI tool action
      - name: Azure Launch
        uses: seqeralabs/action-tower-launch@v2
        if: ${{ matrix.enabled && ( github.event_name != 'workflow_dispatch' || inputs.azure ) }}
        with:
          run_name: sarek_${{ matrix.profile }}
          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
          revision: ${{ github.sha }}
          workdir: ${{ secrets.TOWER_BUCKET_AZURE}}/sarek/work-${{ github.sha }}/${{ matrix.profile }}
          parameters: |
            {
              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
              "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/"
            }
          profiles: ${{ matrix.profile }}

      - uses: actions/upload-artifact@v3
        name: Save Azure Logs
        if: success() || failure()
        with:
          name: tower-azure-${{ matrix.profile }}-log
          path: |
            tower_action_*.log
            tower_action_*.json