Converting Galaxy wf to Nextflow wf #120
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| name: nf-core linting | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'adopt' | |
| java-version: '11' | |
| - name: install Nextflow | |
| run: | | |
| wget -qO- https://get.nextflow.io | bash | |
| chmod +x nextflow | |
| mkdir -p $HOME/.local/bin | |
| mv nextflow $HOME/.local/bin/ | |
| echo "$HOME/.local/bin" >> $GITHUB_PATH | |
| - name: set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.x' | |
| - name: install nf-core tools | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install nf-core | |
| - name: check Nextflow version | |
| run: nextflow -version | |
| # https://nf-co.re/tools/docs/latest/pipeline_lint_tests/ | |
| - name: create .nf-core.yml | |
| run: | | |
| cat << EOF > .nf-core.yml | |
| repository_type: pipeline | |
| lint: | |
| actions_awsfulltest: False | |
| actions_awstest: False | |
| multiqc_config: False | |
| schema_lint: False | |
| schema_params: False | |
| EOF | |
| - name: run nf-core lint | |
| run: nf-core pipelines lint --dir . |