feat: upgrade to use bgcflow wrapper v0.5.0 which use Snakemake v8.25.5 #314
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| name: build-conda-environments | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| build-environments: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| environment: | |
| - workflow/envs/antismash.yaml | |
| #- workflow/envs/antismash_v6.yaml | |
| - workflow/envs/arts.yaml | |
| - workflow/envs/automlst_wrapper.yaml | |
| - workflow/envs/bgc_analytics.yaml | |
| - workflow/envs/bigscape.yaml | |
| - workflow/envs/bigslice.yaml | |
| - workflow/envs/checkm.yaml | |
| - workflow/envs/cblaster.yaml | |
| - workflow/envs/clinker.yaml | |
| - workflow/envs/dbt-duckdb.yaml | |
| - workflow/envs/deeptfactor.yaml | |
| - workflow/envs/eggnog.yaml | |
| - workflow/envs/fastani.yaml | |
| - workflow/envs/gtdbtk.yaml | |
| - workflow/envs/mash.yaml | |
| - workflow/envs/mmseqs2.yaml | |
| - workflow/envs/prokka.yaml | |
| - workflow/envs/r_notebook.yaml | |
| - workflow/envs/roary.yaml | |
| - workflow/envs/seqfu.yaml | |
| - workflow/envs/utilities.yaml | |
| #- workflow/envs/lsabgc.yaml | |
| steps: | |
| - name: Checkout repository and submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Micromamba | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| micromamba-version: '2.0.4-0' | |
| environment-file: ${{ matrix.environment }} | |
| init-shell: bash | |
| cache-environment: true | |
| post-cleanup: 'all' | |
| - name: Test conda environment | |
| run: echo "Testing conda environment" | |
| - name: Fail build if tests fail | |
| run: exit 1 | |
| if: ${{ job.status != 'success' }} |