github-actions.yml

name: DeepRVAT Pipeline tests
run-name: DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬
on: [ push ]

jobs:
  Smoke-RunTraining:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        with:
          environment-name: deeprvat-gh-action
          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
          cache-environment: true
          cache-downloads: true
      - name: Smoke test run_training pipeline
        run: |
          python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
          --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs
        shell: micromamba-shell {0}

  Smoke-RunTraining2:
    uses: ./.github/workflows/setup-deeprvat-env.yaml
    with:
      environment-file: deeprvat_env_no_gpu.yml
      env-name: Smoke-RunTraining
      command: |
          python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
          --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs

  Smoke-Association-Testing-Pretrained:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        with:
          environment-name: deeprvat-gh-action
          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
          cache-environment: true
          cache-downloads: true
      - name: Link pretrained models
        run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
        shell: bash -el {0}
      - name: Smoke test 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 -F
        shell: micromamba-shell {0}

  Smoke-Association-Testing-Training:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        with:
          environment-name: deeprvat-gh-action
          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
          cache-environment: true
          cache-downloads: true
      - name: Link pretrained models
        run: cd ${{ github.workspace }}/example && ln -s ../pretrained_models
        shell: bash -el {0}
      - name: Smoke test 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 -F
        shell: micromamba-shell {0}

  Smoke-Seed-Gene-Discovery:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        with:
          environment-name: deeprvat-gh-action
          environment-file: ${{ github.workspace }}/deeprvat_env_no_gpu.yml
          cache-environment: true
          cache-downloads: true
      - name: Copy seed gene discovery snakemake config
        run: cd ${{ github.workspace }}/example && cp ../deeprvat/seed_gene_discovery/config.yaml .
        shell: bash -el {0}
      - name: Smoke test 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 -F
        shell: micromamba-shell {0}

  Pipeline-Tests-RunTraining:
    runs-on: ubuntu-latest
    needs: Smoke-RunTraining
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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 run_training pipeline
        run: |
          python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
          --snakefile ${{ github.workspace }}/pipelines/run_training.snakefile --show-failed-logs -F
        shell: micromamba-shell {0}

  Pipeline-Tests-Training-Association-Testing:
    runs-on: ubuntu-latest
    needs: Smoke-Association-Testing-Training
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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 -F
        shell: micromamba-shell {0}

  Pipeline-Tests-Association-Testing-Pretrained:
    runs-on: ubuntu-latest
    needs: Smoke-Association-Testing-Pretrained
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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: 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 -F
        shell: micromamba-shell {0}

  Pipeline-Tests-Seed-Gene-Discovery:
    runs-on: ubuntu-latest
    needs: Smoke-Seed-Gene-Discovery
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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: 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 -F
        shell: micromamba-shell {0}

  Smoke-Preprocessing-No-QC:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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}

  Smoke-Preprocessing-With-QC:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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: 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}

  Pipeline-Preprocessing-No-QC:
    runs-on: ubuntu-latest
    needs: Smoke-Preprocessing-No-QC
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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}

  Pipeline-Preprocessing-With-QC:
    runs-on: ubuntu-latest
    needs: Smoke-Preprocessing-With-QC
    steps:

      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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}

  Smoke-Annotation-Pipeline:
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository code
        uses: actions/checkout@v4
      - uses: mamba-org/setup-micromamba@v1.8.1
        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}