DeepRVAT 🧬🧪💻🧑🔬 #724
Workflow file for this run
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
| 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@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| with: | |
| environment-name: deeprvat-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Smoketest training_association_testing pipeline | |
| run: | | |
| python -m snakemake -n -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: Smoketest association_testing_pretrained pipeline | |
| run: | | |
| python -m snakemake -n -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: Smoketest seed_gene_discovery pipeline | |
| run: | | |
| python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \ | |
| --snakefile ${{ github.workspace }}/pipelines/seed_gene_discovery.snakefile --show-failed-logs | |
| shell: micromamba-shell {0} | |
| DeepRVAT-Pipeline-Tests: | |
| runs-on: ubuntu-latest | |
| needs: DeepRVAT-Pipeline-Smoke-Tests | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| 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@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| with: | |
| environment-name: deeprvat-preprocess-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Fake fasta data | |
| if: steps.cache-fasta.outputs.cache-hit != 'true' | |
| run: | | |
| cd ${{ github.workspace }}/example/preprocess && touch workdir/reference/GRCh38.primary_assembly.genome.fa | |
| - name: Run preprocessing pipeline no qc Smoke Test | |
| run: | | |
| python -m snakemake -n -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} | |
| - name: Preprocessing pipeline with qc Smoke Test | |
| run: | | |
| python -m snakemake -n -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} | |
| DeepRVAT-Annotation-Pipeline-Smoke-Tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| with: | |
| environment-name: deeprvat-preprocess-gh-action | |
| environment-file: ${{ github.workspace }}/deeprvat_preprocessing_env.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Annotations Smoke Test | |
| run: | | |
| python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example/annotations \ | |
| --snakefile ${{ github.workspace }}/pipelines/annotations.snakefile \ | |
| --configfile ${{ github.workspace }}/pipelines/config/deeprvat_annotation_config.yaml --show-failed-logs | |
| shell: micromamba-shell {0} | |
| 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@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| 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@v4 | |
| 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@v4 | |
| - uses: mamba-org/setup-micromamba@v1.8.0 | |
| 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@v4 | |
| 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} |