nf-core AWS full size tests #22
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| name: nf-core AWS full size tests | |
| # This workflow is triggered on published releases. | |
| # It can be additionally triggered manually with GitHub actions workflow dispatch. | |
| # It runs the -profile 'test_full' on AWS batch | |
| on: | |
| workflow_run: | |
| workflows: ["nf-core Docker push (release)"] | |
| types: [completed] | |
| workflow_dispatch: | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} | |
| AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} | |
| AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} | |
| AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} | |
| jobs: | |
| run-awstest: | |
| name: Run AWS full tests | |
| if: github.repository == 'nf-core/eager' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: 3.7 | |
| - name: Install awscli | |
| run: conda install -c conda-forge awscli | |
| - name: Start AWS batch job | |
| # Add full size test data (but still relatively small datasets for few samples) | |
| # on the `test_full.config` test runs with only one set of parameters | |
| # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command | |
| run: | | |
| aws batch submit-job \ | |
| --region eu-west-1 \ | |
| --job-name nf-core-eager \ | |
| --job-queue $AWS_JOB_QUEUE \ | |
| --job-definition $AWS_JOB_DEFINITION \ | |
| --container-overrides '{"command": ["nf-core/eager", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/eager/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/eager/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' |