nf-core cloud test #3
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| 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-test: | |
| name: launch | |
| runs-on: ubuntu-latest | |
| if: ${{ github.repository == 'nf-core/sarek' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - profile: test_aws | |
| test: test | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_azure | |
| test: test | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_aws | |
| test: somatic | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_full_azure | |
| test: somatic | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_germline_aws | |
| test: germline | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| - profile: test_full_germline_azure | |
| test: germline | |
| cloud: azure | |
| compute_env: TOWER_CE_AZURE_CPU | |
| workdir: TOWER_BUCKET_AZURE | |
| - profile: test_full_germline_ncbench_agilent | |
| test: germline_ncbench_agilent | |
| cloud: aws | |
| compute_env: TOWER_COMPUTE_ENV | |
| workdir: TOWER_BUCKET_AWS | |
| steps: | |
| # Launch workflow on AWS Batch | |
| - name: Launch | |
| uses: seqeralabs/action-tower-launch@v2 | |
| # If inputs item exists (i.e. workflow_dispatch), then we find matrix.test and check it is false | |
| # If is false, we negate and run the job | |
| if: ( !contains(inputs[matrix.test], 'false') && !contains(inputs[matrix.cloud], 'false') ) | |
| with: | |
| run_name: sarek_${{ matrix.profile }} | |
| workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} | |
| access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| compute_env: ${{ secrets[matrix.compute_env] }} | |
| revision: ${{ github.sha }} | |
| workdir: ${{ secrets[matrix.workdir] }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }} | |
| parameters: | | |
| { | |
| "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", | |
| "outdir": "${{ secrets[matrix.workdir] }}/sarek/results-${{ github.sha }}/${{ matrix.profile }}/" | |
| } | |
| profiles: ${{ matrix.profile }} | |
| - uses: actions/upload-artifact@v3 | |
| name: Save Logs | |
| if: success() || failure() | |
| with: | |
| name: tower-${{ matrix.profile }}-log | |
| path: | | |
| tower_action_*.log | |
| tower_action_*.json |