minor fix for avoid non-matching variants going through allele_qc to throw error in mr #511
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| name: Continuous Integration | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - .github | |
| - .gitignore | |
| - README.md | |
| jobs: | |
| ci_linux-64: | |
| runs-on: ubuntu-latest | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create YAML from recipe | |
| run: | | |
| cp .github/environment/environment.yaml /tmp/environment.yaml | |
| grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: /tmp/environment.yaml | |
| generate-run-shell: true | |
| - name: Run unit tests | |
| shell: micromamba-shell {0} | |
| run: R -e "devtools::test()" | |
| - name: Check unit test code coverage | |
| shell: micromamba-shell {0} | |
| run: R -e "covr::codecov(quiet = FALSE)" | |
| #- name: Run R CMD CHECK | |
| #shell: micromamba-shell {0} | |
| #run: R -e "rcmdcheck::rcmdcheck()" | |
| #- name: Run BiocCheckGitClone | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheckGitClone()" | |
| #- name: Run BiocCheck | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheck()" | |
| ci_osx-64: | |
| runs-on: macos-13 | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create YAML from recipe | |
| run: | | |
| cp .github/environment/environment.yaml /tmp/environment.yaml | |
| grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: /tmp/environment.yaml | |
| generate-run-shell: true | |
| - name: Run unit tests | |
| shell: micromamba-shell {0} | |
| run: R -e "devtools::test()" | |
| #- name: Run R CMD CHECK | |
| #shell: micromamba-shell {0} | |
| #run: R -e "rcmdcheck::rcmdcheck()" | |
| #- name: Run BiocCheckGitClone | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheckGitClone()" | |
| #- name: Run BiocCheck | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheck()" | |
| # | |
| ci_osx-arm64: | |
| runs-on: macos-14 | |
| steps: | |
| - name: Checkout pull request branch | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Create YAML from recipe | |
| run: | | |
| cp .github/environment/environment.yaml /tmp/environment.yaml | |
| grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/ /' >> /tmp/environment.yaml | |
| - name: Setup micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: /tmp/environment.yaml | |
| generate-run-shell: true | |
| - name: Run unit tests | |
| shell: micromamba-shell {0} | |
| run: R -e "devtools::test()" | |
| #- name: Run R CMD CHECK | |
| #shell: micromamba-shell {0} | |
| #run: R -e "rcmdcheck::rcmdcheck()" | |
| #- name: Run BiocCheckGitClone | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheckGitClone()" | |
| #- name: Run BiocCheck | |
| #shell: micromamba-shell {0} | |
| #run: R -e "BiocCheck::BiocCheck()" |