all-bactopia-tool-tests.yml

name: All Bactopia Tests

on: workflow_dispatch
  #schedule:
    # At 01:30 on Monday and Thursday
    #- cron:  '30 1 * * 1,4'

jobs:
  bactopia-tools-tests:
    runs-on: self-hosted
    defaults:
      run:
        shell: bash -l {0}

    steps:
      - name: Checkout bactopia/bactopia
        uses: actions/checkout@v4
        with:
          path: ${{ github.run_id }}/bactopia

      - name: Setup ENV variables
        run: |
          echo "BACTOPIA_CI=/data/storage/bactopia-ci" >> $GITHUB_ENV
          echo "BACTOPIA_CONDA=/data/storage/bactopia-ci/envs/conda" >> $GITHUB_ENV
          echo "BACTOPIA_SINGULARITY=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV
          echo "BACTOPIA_TESTS=/data/storage/bactopia-ci/bactopia-tests/data" >> $GITHUB_ENV
          echo "BACTOPIA_WORKSPACE=${GITHUB_WORKSPACE}/${{ github.run_id }}/bactopia" >> $GITHUB_ENV
          echo "BACTOPIA_TMP=/data/storage/bactopia-tmp/${{ github.run_id }}" >> $GITHUB_ENV
          echo "NXF_SINGULARITY_CACHEDIR=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV
          echo "NXF_SINGULARITY_HOME_MOUNT=true" >> $GITHUB_ENV
          echo "SINGULARITY_CACHEDIR=/data/storage/bactopia-ci/envs/singularity" >> $GITHUB_ENV
          echo "SINGULARITY_TMPDIR=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
          echo "TMP=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
          echo "TMPDIR=/data/storage/bactopia-tmp/${{ github.run_id }}/tmp" >> $GITHUB_ENV
          mkdir -p "/data/storage/bactopia-tmp/${{ github.run_id }}/tmp"
          chmod -R 777 "/data/storage/bactopia-tmp/${{ github.run_id }}"

      - name: Singularity Profile
        run: |
          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
          conda activate bactopia-ci
          cd ${{ env.BACTOPIA_WORKSPACE }}
          ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \
              bash -c 'BACTOPIA_ARGS="-profile singularity --singularity_pull_docker_container --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'

      - name: Docker Profile
        run: |
          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
          conda activate bactopia-ci
          cd ${{ env.BACTOPIA_WORKSPACE }}
          ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \
              bash -c 'BACTOPIA_ARGS="-profile docker --is_ci --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'

      - name: Conda Profile
        run: |
          source /data/storage/bactopia-ci/miniforge/etc/profile.d/conda.sh
          conda activate bactopia-ci
          conda clean --all -y
          cd ${{ env.BACTOPIA_WORKSPACE }}
          ls subworkflows/local/ | grep -v -E "teton" | xargs -I {} -P 20 \
              bash -c 'BACTOPIA_ARGS="--is_ci --condadir ${{ env.BACTOPIA_CONDA }} --test_data_dir ${{ env.BACTOPIA_TESTS }}" TMPDIR=${{ env.BACTOPIA_TMP }} \
                       pytest --wt 5 --symlink --kwdof -o "testpaths=tests subworkflows/local/" --git-aware --tag {}'

      - name: Upload logs on failure
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: logs-bactopia-tools
          path: |
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.out
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/log.err
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/.nextflow.log
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.log
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.err
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*.out
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stderr.txt
            ${{ env.BACTOPIA_TMP }}/pytest_workflow_*/*/work/**/*stdout.txt
            
      - name: Cleanup
        if: always()
        run: rm -rf ${GITHUB_WORKSPACE}/${{ github.run_id }} ${{ env.BACTOPIA_TMP }}