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Update config to fix missing bypass_ashleys parameter and GH actions
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| name: MosaiCatcher assemblies checks | ||
|
|
||
| on: | ||
| push: | ||
| branches: | ||
| - "**" | ||
| 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: Pull LFS objects in submodules | ||
| run: git submodule foreach --recursive 'git lfs pull' | ||
|
|
||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=hg38 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-hg19: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Pull LFS objects in submodules | ||
| run: git submodule foreach --recursive 'git lfs pull' | ||
|
|
||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=hg19 use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-T2T: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Pull LFS objects in submodules | ||
| run: git submodule foreach --recursive 'git lfs pull' | ||
|
|
||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$CONDA/bin" >> $GITHUB_PATH | ||
|
|
||
| - name: Install dependencies | ||
| run: conda install -c conda-forge mamba | ||
|
|
||
| - name: Setup Snakemake | ||
| run: mamba install -c conda-forge -c bioconda snakemake==7.32.4 | ||
|
|
||
| - name: List options of workflow | ||
| run: | | ||
| snakemake --cores 1 --config list_commands=True --verbose --debug | ||
| - name: Run workflow | ||
| run: | | ||
| snakemake --cores 1 --use-conda --config reference=T2T use_light_data=True chromosomes=[chr17] ashleys_pipeline=True \ | ||
| --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile | ||
| Testing-with-mm10: | ||
| runs-on: ubuntu-latest | ||
| needs: | ||
| - Formatting | ||
| - Linting | ||
| - Testing-basic-v7 | ||
| - Testing-basic-with-ashleys | ||
| # - Testing-basic-with-slurm | ||
| steps: | ||
| - name: Checkout repository with submodules and LFS | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| lfs: true | ||
|
|
||
| - name: Pull LFS objects in submodules | ||
| run: git submodule foreach --recursive 'git lfs pull' | ||
|
|
||
| - name: Setup Python | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Add Conda to system path | ||
| run: echo "$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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