Add support for octal and comma separated samtools exclude flags (#113) #731
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| 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: ${GITHUB_WORKSPACE}/../CRISPResso2_copy | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Conda Env | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: test_env | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: false | |
| use-mamba: true | |
| - name: Get Date | |
| run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT | |
| shell: bash | |
| - name: Cache Conda Env | |
| id: cache-env | |
| uses: actions/cache@v3 | |
| env: | |
| # Increase this number to reset the cache if envs/test_env.yml hasn't changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: /usr/share/miniconda/envs/test_env | |
| key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('.github/envs/test_env.yml') }} | |
| - name: Update Conda Env | |
| run: | | |
| conda env update -n test_env -f .github/envs/test_env.yml | |
| if: steps.cache-env.outputs.cache-hit != 'true' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl | |
| conda list | |
| - 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 | |
| # ref: '<BRANCH-NAME>' # update to specific branch | |
| - name: Run Basic | |
| run: | | |
| make basic test print | |
| - name: Run Params | |
| if: success() || failure() | |
| run: | | |
| make params test print | |
| - name: Run Prime Editor | |
| if: success() || failure() | |
| run: | | |
| make prime-editor test print | |
| - name: Run BAM Input | |
| if: success() || failure() | |
| run: | | |
| make bam test print | |
| - name: Run BAM Output | |
| if: success() || failure() | |
| run: | | |
| make bam-out test print | |
| - name: Run BAM Genome Output | |
| if: success() || failure() | |
| run: | | |
| make bam-out-genome test print | |
| - name: Run Batch | |
| if: success() || failure() | |
| run: | | |
| make batch test print | |
| - name: Run Pooled | |
| if: success() || failure() | |
| run: | | |
| make pooled test print | |
| - name: Run Pooled Mixed Mode | |
| if: success() || failure() | |
| run: | | |
| make pooled-mixed-mode test print | |
| - name: Run Pooled Mixed Mode Demux | |
| if: success() || failure() | |
| run: | | |
| make pooled-mixed-mode-genome-demux test print | |
| - name: Run Pooled Paired Sim | |
| if: success() || failure() | |
| run: | | |
| make pooled-paired-sim test print | |
| - name: Run WGS | |
| if: success() || failure() | |
| run: | | |
| make wgs test print | |
| - name: Run Compare | |
| if: success() || failure() | |
| run: | | |
| make compare test print | |
| - name: Run Aggregate | |
| if: success() || failure() | |
| run: | | |
| make aggregate test print |