From 26b953397d08dad122af027fb14ea943ce7f9ad9 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Wed, 3 Jun 2026 17:41:22 +0200 Subject: [PATCH 1/5] chore: use github-status logger plugin --- .github/workflows/main.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index f2dbaf2..bf68380 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -99,10 +99,13 @@ jobs: 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 + --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 From b7726bb998eb2a057a6506d90e0827b99b1b85ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 10 Jun 2026 10:07:56 +0200 Subject: [PATCH 2/5] Add permissions to evaluate job in workflow --- .github/workflows/main.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index bf68380..d749f3a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -40,6 +40,9 @@ jobs: evaluate: needs: setup runs-on: ubuntu-latest + permissions: + statuses: write + contents: read strategy: fail-fast: false matrix: From f1370bb2a4aee2e6113342fa1c21ca8ec0f99d71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 10 Jun 2026 10:41:54 +0200 Subject: [PATCH 3/5] Add GITHUB_TOKEN to Snakemake action --- .github/workflows/main.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d749f3a..6781d9c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -96,6 +96,8 @@ jobs: - name: Run analysis uses: snakemake/snakemake-github-action@v2.1.1 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} with: directory: "." snakefile: "workflow/Snakefile" From e951a006bb60664fb6f045f6fd49fb4fd304acdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 10 Jun 2026 10:45:19 +0200 Subject: [PATCH 4/5] Enable concurrency for CI workflow --- .github/workflows/main.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 6781d9c..d682975 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -7,9 +7,9 @@ on: workflow_dispatch: # DBG, check if concurrency is the issue -#concurrency: -# group: ci-${{ 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: ${{ secrets.FTP_PASSWORD }} From 239d9826810dfa562eb80a17fa244675448a7453 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 10 Jun 2026 14:07:00 +0200 Subject: [PATCH 5/5] Add verbose flag to benchmark command Added verbosity to the benchmark command in the workflow. --- .github/workflows/main.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d682975..0d4a624 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -105,7 +105,7 @@ jobs: benchmark_all --config benchmark=${{ matrix.sample }} --cores 4 --sdm conda --conda-cleanup-pkgs cache - --rerun-triggers mtime --all-temp + --rerun-triggers mtime --all-temp --verbose --logger github-status --logger-github-status-run-name ${{ matrix.sample }} stagein: | pip install snakemake-storage-plugin-zenodo