Unset env variable JAVA_TOOL_OPTIONS in gitpod #6741
Workflow file for this run
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| name: Create a pipeline and run nf-core linting | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| pull_request: | |
| release: | |
| types: [published] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_ANSI_LOG: false | |
| jobs: | |
| MakeTestWorkflow: | |
| runs-on: self-hosted | |
| env: | |
| NXF_ANSI_LOG: false | |
| strategy: | |
| matrix: | |
| NXF_VER: | |
| - "23.04.0" | |
| - "latest-everything" | |
| steps: | |
| # Get the repo code | |
| - uses: actions/checkout@v4 | |
| name: Check out source-code repository | |
| # Set up nf-core/tools | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Install python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| # Set up Nextflow | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: ${{ matrix.NXF_VER }} | |
| # Install the Prettier linting tools | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| # Install the editorconfig linting tools | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| # Build a pipeline from the template | |
| - name: nf-core create | |
| run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain | |
| # Try syncing it before we change anything | |
| - name: nf-core sync | |
| run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/ | |
| # Build a module from the template | |
| - name: nf-core modules create | |
| run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta | |
| # Run code style linting | |
| - name: Run Prettier --check | |
| run: prettier --check nf-core-testpipeline | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') | |
| # Update modules to the latest version | |
| - name: nf-core modules update | |
| run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview | |
| # Remove TODO statements | |
| - name: remove TODO | |
| run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; | |
| # Replace zenodo.XXXXXX to pass readme linting | |
| - name: replace zenodo.XXXXXX | |
| run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; | |
| # Run nf-core linting | |
| - name: nf-core lint | |
| run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned | |
| # Run the other nf-core commands | |
| - name: nf-core list | |
| run: nf-core --log-file log.txt list | |
| # - name: nf-core licences | |
| # run: nf-core --log-file log.txt licences nf-core-testpipeline | |
| - name: nf-core schema | |
| run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts | |
| - name: nf-core bump-version | |
| run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1 | |
| - name: nf-core lint in release mode | |
| run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release | |
| - name: nf-core modules install | |
| run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force | |
| - name: nf-core modules install gitlab | |
| run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/ | |
| - name: nf-core modules list local | |
| run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/ | |
| - name: nf-core modules list remote | |
| run: nf-core --log-file log.txt modules list remote | |
| - name: nf-core modules list remote gitlab | |
| run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote | |
| - name: Upload log file artifact | |
| if: ${{ always() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: nf-core-log-file | |
| path: log.txt |