DeepRVAT 🧬🧪💻🧑🔬 #372
Workflow file for this run
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| name: DeepRVAT | |
| run-name: DeepRVAT 🧬🧪💻🧑🔬 | |
| on: [ push ] | |
| jobs: | |
| DeepRVAT-Pipeline-Smoke-Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Training Association Testing smoke test | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: 'example' | |
| snakefile: 'pipelines/training_association_testing.snakefile' | |
| args: '-j 2 -n' | |
| - name: Link pretrained models | |
| run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models | |
| - name: Association Testing Pretrained Smoke Test | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: 'example' | |
| snakefile: 'pipelines/association_testing_pretrained.snakefile' | |
| args: '-j 2 -n' | |
| - name: Seed Gene Discovery Smoke Test | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: 'example' | |
| snakefile: 'pipelines/seed_gene_discovery.snakefile' | |
| args: '-j 2 -n' | |
| DeepRVAT-Pipeline-Tests: | |
| runs-on: ubuntu-latest | |
| needs: DeepRVAT-Pipeline-Smoke-Tests | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1.4.3 | |
| with: | |
| environment-name: deeprvat-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Install DeepRVAT | |
| run: pip install -e ${{ github.workspace }} | |
| shell: micromamba-shell {0} | |
| # There are no GPUs on the gh worker, so we disable it in the config | |
| - name: Update config to use no gpus | |
| run: "sed -i 's/gpus: 1/gpus: 0/' ${{ github.workspace }}/example/config.yaml" | |
| shell: bash -el {0} | |
| - name: Run training_association_testing pipeline | |
| run: | | |
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example \ | |
| --snakefile ${{ github.workspace }}/pipelines/training_association_testing.snakefile --show-failed-logs | |
| shell: micromamba-shell {0} | |
| - name: Link pretrained models | |
| run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models | |
| shell: bash -el {0} | |
| - name: Run association_testing_pretrained pipeline | |
| run: | | |
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example \ | |
| --snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained.snakefile --show-failed-logs | |
| shell: micromamba-shell {0} | |
| - name: Copy seed gene discovery snakemake config | |
| run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml . | |
| shell: bash -el {0} | |
| - name: Run seed_gene_discovery pipeline | |
| run: | | |
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example \ | |
| --snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs | |
| shell: micromamba-shell {0} | |
| DeepRVAT-Preprocessing-Pipeline-Smoke-Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Preprocessing Smoke Test With QC | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: 'example/preprocess' | |
| snakefile: 'pipelines/preprocess_with_qc.snakefile' | |
| args: '-j 2 -n --configfile pipelines/config/deeprvat_preprocess_config.yaml' | |
| stagein: 'touch example/preprocess/workdir/reference/GRCh38.primary_assembly.genome.fa' | |
| - name: Preprocessing Smoke Test No QC | |
| uses: snakemake/snakemake-github-action@v1.24.0 | |
| with: | |
| directory: 'example/preprocess' | |
| snakefile: 'pipelines/preprocess_no_qc.snakefile' | |
| args: '-j 2 -n --configfile pipelines/config/deeprvat_preprocess_config.yaml' | |
| stagein: 'touch example/preprocess/workdir/reference/GRCh38.primary_assembly.genome.fa' | |
| DeepRVAT-Annotation-Pipeline-Smoke-Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - name: Annotations Smoke Test | |
| uses: snakemake/snakemake-github-action@v1.25.1 | |
| with: | |
| directory: 'example/annotations' | |
| snakefile: 'pipelines/annotations.snakefile' | |
| args: '-j 2 -n --configfile pipelines/config/deeprvat_annotation_config.yaml' | |
| DeepRVAT-Preprocessing-Pipeline-Tests-No-QC: | |
| runs-on: ubuntu-latest | |
| needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1.4.3 | |
| with: | |
| environment-name: deeprvat-preprocess-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Install DeepRVAT | |
| run: pip install -e ${{ github.workspace }} | |
| shell: micromamba-shell {0} | |
| - name: Cache Fasta file | |
| id: cache-fasta | |
| uses: actions/cache@v3 | |
| with: | |
| path: example/preprocess/workdir/reference | |
| key: ${{ runner.os }}-reference-fasta | |
| - name: Download and unpack fasta data | |
| if: steps.cache-fasta.outputs.cache-hit != 'true' | |
| run: | | |
| cd ${{ github.workspace }}/example/preprocess && \ | |
| wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \ | |
| -O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \ | |
| && gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz | |
| - name: Run preprocessing pipeline | |
| run: | | |
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \ | |
| --snakefile ${{ github.workspace }}/pipelines/preprocess_no_qc.snakefile \ | |
| --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs | |
| shell: micromamba-shell {0} | |
| DeepRVAT-Preprocessing-Pipeline-Tests-With-QC: | |
| runs-on: ubuntu-latest | |
| needs: DeepRVAT-Preprocessing-Pipeline-Smoke-Tests | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@v1.4.3 | |
| with: | |
| environment-name: deeprvat-preprocess-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Install DeepRVAT | |
| run: pip install -e ${{ github.workspace }} | |
| shell: micromamba-shell {0} | |
| - name: Cache Fasta file | |
| id: cache-fasta | |
| uses: actions/cache@v3 | |
| with: | |
| path: example/preprocess/workdir/reference | |
| key: ${{ runner.os }}-reference-fasta | |
| - name: Download and unpack fasta data | |
| if: steps.cache-fasta.outputs.cache-hit != 'true' | |
| run: | | |
| cd ${{ github.workspace }}/example/preprocess && \ | |
| wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz \ | |
| -O workdir/reference/GRCh38.primary_assembly.genome.fa.gz \ | |
| && gzip -d workdir/reference/GRCh38.primary_assembly.genome.fa.gz | |
| - name: Run preprocessing pipeline | |
| run: | | |
| python -m snakemake -j 2 --directory ${{ github.workspace }}/example/preprocess \ | |
| --snakefile ${{ github.workspace }}/pipelines/preprocess_with_qc.snakefile \ | |
| --configfile ${{ github.workspace }}/pipelines/config/deeprvat_preprocess_config.yaml --show-failed-logs | |
| shell: micromamba-shell {0} |