diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f2dbaf2..0d4a624 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -7,9 +7,9 @@ on: workflow_dispatch: # DBG, check if concurrency is the issue -#concurrency: -# group: ci-${{ github.head_ref || github.run_id }} -# cancel-in-progress: true +concurrency: + group: ci-${{ github.head_ref || github.run_id }} + cancel-in-progress: true env: FTP_PASSWORD: ${{ secrets.FTP_PASSWORD }} @@ -40,6 +40,9 @@ jobs: evaluate: needs: setup runs-on: ubuntu-latest + permissions: + statuses: write + contents: read strategy: fail-fast: false matrix: @@ -93,16 +96,21 @@ jobs: - name: Run analysis uses: snakemake/snakemake-github-action@v2.1.1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} with: directory: "." snakefile: "workflow/Snakefile" args: > benchmark_all --config benchmark=${{ matrix.sample }} - --cores 4 --sdm conda --conda-cleanup-pkgs cache --rerun-triggers mtime --all-temp + --cores 4 --sdm conda --conda-cleanup-pkgs cache + --rerun-triggers mtime --all-temp --verbose + --logger github-status --logger-github-status-run-name ${{ matrix.sample }} stagein: | pip install snakemake-storage-plugin-zenodo pip install snakemake-storage-plugin-http + pip install snakemake-logger-plugin-github-status - name: Upload results uses: actions/upload-artifact@v4