MosaiCatcher advanced modules checks #7
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| name: MosaiCatcher advanced modules checks | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| logLevel: | |
| description: "Log level" | |
| required: true | |
| default: "warning" | |
| type: choice | |
| options: | |
| - info | |
| - warning | |
| - debug | |
| schedule: | |
| - cron: "0 0 * * 0" | |
| jobs: | |
| Testing-with-MultiQC: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| # - Testing-basic-v7 | |
| # - Testing-basic-with-ashleys | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # lfs: true | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | |
| Testing-with-ms-norm: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| # - Testing-basic-v7 | |
| # - Testing-basic-with-ashleys | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # lfs: true | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | |
| Testing-with-breakpointR-only: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| # - Testing-basic-v7 | |
| # - Testing-basic-with-ashleys | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # lfs: true | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | |
| Testing-with-whatshap-only: | |
| runs-on: ubuntu-latest | |
| # needs: | |
| # - Formatting | |
| # - Linting | |
| # - Testing-basic-v7 | |
| # - Testing-basic-with-ashleys | |
| steps: | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| # lfs: true | |
| - name: Git Submodule Update | |
| run: | | |
| # git pull --recurse-submodules | |
| git submodule update --remote --recursive --force --init | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.12" | |
| - name: Add Conda to system path | |
| run: echo "$CONDA/bin" >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: conda install -c conda-forge mamba | |
| - name: Setup Snakemake | |
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | |
| - name: List options of workflow | |
| run: | | |
| snakemake --cores 1 --config list_commands=True --verbose --debug | |
| - name: Run workflow | |
| run: | | |
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \ | |
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile |