VIPERA/.github/workflows/test_v9.yml at 20ab5781850025781eaecdd74a24adf7c0e189b3 · PathoGenOmics-Lab/VIPERA · GitHub

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name: Test Sm v9

on:
  workflow_dispatch:
  push:
    branches:
      - main
      - dev
  pull_request:
    branches:
      - "**"

jobs:
  run_test_pipeline:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3
      - name: Setup environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          channel-priority: strict
          activate-environment: snakemake
          auto-activate-base: false
          miniforge-version: latest
          environment-file: .test/environment_v9.yaml
      - name: Run test pipeline
        shell: bash -el {0}
        run: snakemake --snakefile .test/Snakefile --configfile config/config.yaml .test/targets.yaml -c1 --sdm conda --keep-going --notemp
      - name: Pack logs
        if: success() || failure()
        shell: bash -el {0}
        run: tar czf logs.tar.gz .test/output .snakemake/log
      - name: Upload output file
        if: success() || failure()
        uses: actions/upload-artifact@v4
        with:
          name: output-logs
          path: logs.tar.gz