nawf config: new augs #44
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| Formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Formatting | |
| uses: github/super-linter@v4 | |
| env: | |
| VALIDATE_ALL_CODEBASE: false | |
| DEFAULT_BRANCH: main | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
| Testing: | |
| runs-on: ubuntu-latest | |
| needs: Formatting | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 # we need tags for versioneer to work | |
| - name: Setup NART environment | |
| run: | | |
| wget -O Mambaforge.sh https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh --quiet | |
| bash Mambaforge.sh -b -p "${HOME}/conda" | |
| source "${HOME}/conda/etc/profile.d/conda.sh" | |
| source "${HOME}/conda/etc/profile.d/mamba.sh" | |
| # ensure that mamba is happy to write into the cache | |
| sudo chown -R runner:docker "${HOME}/conda/pkgs/cache" | |
| conda config --set channel_priority flexible | |
| mamba env create -q --name nart --file env.yaml | |
| - name: Install NART | |
| run: | | |
| export PATH="${HOME}/conda/bin:$PATH" | |
| source activate nart | |
| pip install --editable . | |
| nawf -h | |
| nawf config -h | |
| nawf run -h | |
| nart -h | |
| nart monitor -h | |
| nart run -h | |
| nart visual -h | |
| - name: Dry-run NAWF | |
| run: | | |
| export PATH="${HOME}/conda/bin:$PATH" | |
| source activate nart | |
| nawf config -b nart/workflow/resources/data/raw.fastq.gz -d tests/Database -w tests | |
| nawf run all -w tests -n |