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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| 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 | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-ms-norm: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| steps: | ||
| - name: Checkout repository with submodules | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| # lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-breakpointR-only: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| steps: | ||
| - name: Checkout repository with submodules | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| # lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-whatshap-only: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| steps: | ||
| - name: Checkout repository with submodules | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| # lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,189 @@ | ||
| name: MosaiCatcher assemblies checks | ||
|
|
||
| on: | ||
| workflow_dispatch: | ||
| inputs: | ||
| logLevel: | ||
| description: "Log level" | ||
| required: true | ||
| default: "warning" | ||
| type: choice | ||
| options: | ||
| - info | ||
| - warning | ||
| - debug | ||
| schedule: | ||
| - cron: "0 0 * * 0" | ||
|
|
||
| jobs: | ||
| Testing-with-hg38: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-hg19: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-T2T: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-mm10: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Git Submodule Update | ||
| run: | | ||
| git pull --recurse-submodules | ||
| git submodule update --remote --recursive | ||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$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 --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile |
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