sort genes of interest alphabetically #315
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| name: Continuous Integration | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| # This is needed for miniconda, see: | |
| # https://github.com/marketplace/actions/setup-miniconda#important. | |
| shell: bash -l {0} | |
| jobs: | |
| quick-tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| test: | |
| - sanity | |
| - dry-run | |
| - utilities | |
| - report | |
| - scripts | |
| - docs | |
| steps: | |
| - uses: actions/checkout@v2.3.4 # https://github.com/actions/checkout. | |
| with: | |
| submodules: recursive | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: HAMLET | |
| use-mamba: true | |
| - name: Install singularity | |
| uses: eWaterCycle/setup-singularity@v6 | |
| with: | |
| singularity-version: 3.6.4 | |
| # This is used to invalidate the conda environment every week | |
| - name: Get year and week (for conda cache) | |
| id: get-date | |
| run: echo "::set-output name=week::$(/bin/date -u '+%Y-w%V')" | |
| shell: bash | |
| - name: Cache conda environment | |
| id: conda-cache | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ hashFiles('environment.yml') }}-${{ steps.get-date.outputs.week }}-${{ env.CACHE_NUMBER }} | |
| - name: Update HAMLET environment | |
| run: mamba env update -n HAMLET -f environment.yml | |
| if: steps.conda-cache.outputs.cache-hit != 'true' | |
| - name: Run test in conda environment | |
| run: >- | |
| pytest --keep-workflow-wd-on-fail | |
| --tag ${{ matrix.test }} | |
| - name: Check pytest stdout messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp -name log.out); | |
| do echo $file; cat $file; done' | |
| - name: Check pytest stderr messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp -name log.err); | |
| do echo $file; cat $file; done' | |
| functional-tests: | |
| needs: quick-tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| module: | |
| - qc-seq | |
| - snv-indels | |
| - itd | |
| - fusion | |
| - test-hamlet-targetted-RNA | |
| - test-hamlet-chrM | |
| steps: | |
| - name: Maximise build space | |
| uses: easimon/maximize-build-space@master | |
| with: | |
| root-reserve-mb: 30720 | |
| swap-size-mb: 1024 | |
| remove-android: 'true' | |
| remove-dotnet: 'true' | |
| remove-codeql: 'true' | |
| - uses: actions/checkout@v2.3.4 # https://github.com/actions/checkout. | |
| with: | |
| submodules: recursive | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: HAMLET | |
| use-mamba: true | |
| # This is used to invalidate the conda environment every week | |
| - name: Get week number | |
| id: get-date | |
| run: echo "::set-output name=week::$(/bin/date -u '+%Y-w%V')" | |
| shell: bash | |
| - name: Cache conda environment | |
| id: conda-cache | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: conda-${{ hashFiles('environment.yml') }}-${{ steps.get-date.outputs.week }}-${{ env.CACHE_NUMBER }} | |
| - name: Update HAMLET environment | |
| run: mamba env update -n HAMLET -f environment.yml | |
| if: steps.conda-cache.outputs.cache-hit != 'true' | |
| - name: Install singularity | |
| uses: eWaterCycle/setup-singularity@v6 | |
| with: | |
| singularity-version: 3.6.4 | |
| - name: Cache singularity images | |
| uses: actions/cache@v3 | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: | |
| ~/.singularity/cache/snakemake | |
| key: singularity-${{ hashFiles('**/common.smk') }}-${{ matrix.module}}-${{ env.CACHE_NUMBER }} | |
| restore-keys: | | |
| singularity-${{ hashFiles('**/common.smk') }}- | |
| singularity- | |
| - name: Run test in conda environment | |
| run: >- | |
| pytest --keep-workflow-wd-on-fail | |
| --tag ${{ matrix.module}} | |
| --tag functional | |
| - name: Check pytest stdout messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp -name log.out); | |
| do echo $file; cat $file; done' | |
| - name: Check pytest stderr messages in case of failure | |
| if: ${{ failure() }} | |
| run: >- | |
| bash -c ' | |
| for file in $(find /tmp -name log.err); | |
| do echo $file; cat $file; done' |