Update human_pathogen_genomics.md #963
Workflow file for this run
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| name: Validation of the tools and page metadata | |
| on: | |
| pull_request: | |
| branches: [ master, main ] | |
| schedule: | |
| - cron: '0 13 * * 1' | |
| workflow_dispatch: | |
| jobs: | |
| validation: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruamel.yaml requests python-frontmatter | |
| - name: Run tool table 2 yaml | |
| run: | | |
| python var/tools_validator.py | |
| registry-lookup: | |
| if: | | |
| github.repository_owner == 'elixir-europe' && github.event_name != 'pull_request' | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ruamel.yaml requests python-frontmatter | |
| - name: Run regsitry lookup for the tools file | |
| run: | | |
| python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}" | |
| - name: Update markdown pages with DSW links | |
| run: | | |
| python var/dsw_integration.py | |
| - name: Get faircookbook-rdmkit repository | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: elixir-europe/faircookbook-rdmkit | |
| path: faircookbook-rdmkit | |
| ref: main | |
| - name: Update markdown pages with FAIR Cookbook links | |
| run: | | |
| python var/faircookbook_integration.py ${GITHUB_WORKSPACE}/faircookbook-rdmkit/faircookbook_rdmkit_mapping.yml | |
| - name: Deleting faircookbook-rdmkit repository | |
| run: | | |
| rm -r faircookbook-rdmkit | |
| - name: Show differences | |
| run: | | |
| git diff --stat | |
| - name: Create Pull Request | |
| id: cpr | |
| uses: peter-evans/create-pull-request@v3 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| commit-message: Update tool/resource_list.yaml | |
| title: 'Automatic tool/resource-list update' | |
| body: | | |
| This PR is automatically generated based on changes in the main_tool_and_resource_list.csv file or based on new links made between the tool table and TeSS. | |
| Please verify if these changes are valid. | |
| labels: | | |
| automatic PR | |
| reviewers: bedroesb | |
| branch: list_updates | |
| base: master | |
| - name: Check output | |
| run: | | |
| echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}" |