Skip to content

chore: use github-status logger plugin #65

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
johanneskoester merged 5 commits into from
Jun 13, 2026
Merged

chore: use github-status logger plugin #65

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
26b9533
chore: use github-status logger plugin
johanneskoester Jun 3, 2026
b7726bb
Add permissions to evaluate job in workflow
johanneskoester Jun 10, 2026
f1370bb
Add GITHUB_TOKEN to Snakemake action
johanneskoester Jun 10, 2026
e951a00
Enable concurrency for CI workflow
johanneskoester Jun 10, 2026
239d982
Add verbose flag to benchmark command
johanneskoester Jun 10, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 12 additions & 4 deletions .github/workflows/main.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand Down Expand Up @@ -40,6 +40,9 @@ jobs:
evaluate:
needs: setup
runs-on: ubuntu-latest
permissions:
statuses: write
contents: read
strategy:
fail-fast: false
matrix:
Expand Down Expand Up @@ -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
Expand Down
Loading