Decrease Docker image size and fix PE naming and parameter behavior #9
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run Integration Tests | |
| on: | |
| push: | |
| pull_request: | |
| types: [opened, reopened] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: false | |
| activate-environment: test_env | |
| environment-file: .github/envs/test_env.yml | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl | |
| pip install ydiff | |
| - name: Create directory for files | |
| run: | | |
| mkdir ../CRISPResso2_copy | |
| cp -r * ../CRISPResso2_copy | |
| - name: Copy C2_tests repo | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: edilytics/CRISPResso2_tests | |
| token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }} | |
| # ref: '<BRANCH_NAME>' // Use this to specify a branch other than master | |
| - name: Run Basic | |
| run: | | |
| make basic test | |
| - name: Run Params | |
| if: success() || failure() | |
| run: | | |
| make params test | |
| - name: Run Prime Editor | |
| if: success() || failure() | |
| run: | | |
| make prime-editor test | |
| - name: Run Batch | |
| if: success() || failure() | |
| run: | | |
| make batch test | |
| - name: Run Pooled | |
| if: success() || failure() | |
| run: | | |
| make pooled test | |
| - name: Run WGS | |
| if: success() || failure() | |
| run: | | |
| make wgs test | |
| - name: Run Compare | |
| if: success() || failure() | |
| run: | | |
| make compare test |