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DeepRVAT Pipeline tests

DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬 #813

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DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬

DeepRVAT Pipeline tests 🧬🧪💻🧑‍🔬 #813

Workflow file for this run

.github/workflows/github-actions.yml at 8b70ee8
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-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-Pretrained-Regenie:
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_regenie pipeline
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained_regenie.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-Association-Testing-Training-Regenie:
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_regenie pipeline
run: |
python -m snakemake -n -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained_regenie.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-Training-Association-Testing-Regenie:
runs-on: ubuntu-latest
needs: Smoke-Association-Testing-Training-Regenie
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_regenie pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/training_association_testing_regenie.snakefile --show-failed-logs -F
shell: micromamba-shell {0}
Pipeline-Tests-Association-Testing-Pretrained-Regenie:
runs-on: ubuntu-latest
needs: Smoke-Association-Testing-Pretrained-Regenie
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_regenie pipeline
run: |
python -m snakemake -j 2 --directory ${{ github.workspace }}/example \
--snakefile ${{ github.workspace }}/pipelines/association_testing_pretrained_regenie.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}