CI Integration

The CLI exits with meaningful codes (0 = clean, 1 = issues, 2 = error), making it easy to wire into automated pipelines.

GitHub Actions

Add a validation step to any workflow that touches SampleSheet.csv:

# .github/workflows/validate-samplesheet.yml
name: Validate SampleSheet

on:
  push:
    paths:
      - '**/SampleSheet.csv'
  pull_request:
    paths:
      - '**/SampleSheet.csv'

jobs:
  validate:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - uses: actions/setup-python@v5
        with:
          python-version: '3.12'

      - run: pip install "samplesheet-parser[cli]"

      - name: Validate SampleSheet
        run: samplesheet validate SampleSheet.csv --format json

pre-commit hook

Gate commits that touch any SampleSheet.csv in the repository:

# .pre-commit-config.yaml
repos:
  - repo: local
    hooks:
      - id: samplesheet-validate
        name: Validate SampleSheet.csv
        entry: samplesheet validate
        language: python
        additional_dependencies: ["samplesheet-parser[cli]"]
        files: SampleSheet\.csv$
        pass_filenames: true

Install and run once to verify:

pip install pre-commit
pre-commit install
pre-commit run samplesheet-validate --all-files

Stricter Hamming distance in CI

If your lab uses longer indexes (10 bp+), raise the minimum Hamming distance threshold to catch borderline cases earlier:

samplesheet validate SampleSheet.csv --min-hamming 4

Using JSON output in scripts

All commands support --format json for machine-readable output:

result=$(samplesheet validate SampleSheet.csv --format json)
is_valid=$(echo "$result" | python3 -c "import sys,json; print(json.load(sys.stdin)['is_valid'])")

if [ "$is_valid" != "True" ]; then
  echo "SampleSheet validation failed"
  exit 1
fi