Ncbench #15
Workflow file for this run
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| name: NCBench Zenodo Upload | |
| # This workflow can be triggered manually with the GitHub actions workflow dispatch button. | |
| on: | |
| # upload can only be triggered manually for now | |
| workflow_dispatch: | |
| inputs: | |
| germline_wes: | |
| description: "Trigger NCBench upload" | |
| type: boolean | |
| default: true | |
| pull_request: | |
| jobs: | |
| ncbench-upload: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - profile: germline_wes | |
| enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline_wes ) }} | |
| env: | |
| pipeline_version: 3.2.3 | |
| steps: | |
| - name: Download files from AWS | |
| uses: keithweaver/[email protected] | |
| if: ${{ matrix.enabled }} | |
| with: | |
| source: s3://nf-core-awsmegatests/sarek/results-test-59026dc07633edb83aab3bfb2f65f79db38437a1/test_full/variant_calling/strelka | |
| command: sync | |
| aws_region: eu-west-1 | |
| destination: ./variant_calling | |
| flags: --no-sign-request --include ".vcf.gz" --exclude "g.vcf.gz" | |
| - name: Download metadata file for Zenodo | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: FriederikeHanssen/sarek | |
| ref: ncbench | |
| path: sarek-ncbench/ | |
| #- name: Create new Zenodo entry | |
| # uses: popperized/zenodo/create@master | |
| # env: | |
| # ZENODO_METADATA_PATH: sarek-ncbench/assets/zenodo_ncbench.json | |
| # ZENODO_USE_SANDBOX: true | |
| # with: | |
| # secrets: ${{ secrets.ZENODO_API_TOKEN }} | |
| #- name: Upload file to Zenodo | |
| # uses: popperized/zenodo/upload@master | |
| # env: | |
| # ZENODO_DEPOSIT_ID: #TODO get the dposit ID from the previous step | |
| # ZENODO_UPLOAD_PATH: ./variant_calling_v$pipeline_version | |
| # ZENODO_USE_SANDBOX: true | |
| # with: | |
| # secrets: ${{ secrets.ZENODO_API_TOKEN }} | |
| - name: Install jq | |
| uses: sergeysova/jq-action@v2 | |
| - name: NCBench set config | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: FriederikeHanssen/ncbench-workflow | |
| path: ncbench-workflow/ | |
| ref: main | |
| - name: Add entries to config | |
| run: | | |
| jq --help |