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Merge pull request #75 from uab-cgds-worthey/cicd_system_testing
Adds system testing workflow to github actions
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| name: system_testing | ||
| on: | ||
| push: | ||
| paths: | ||
| - ".github/workflows/system_testing.yml" | ||
| - ".test/**" | ||
| - "configs/**" | ||
| - "src/**" | ||
| - "workflow/**" | ||
| pull_request: | ||
| paths: | ||
| - ".github/workflows/system_testing.yml" | ||
| - ".test/**" | ||
| - "configs/**" | ||
| - "src/**" | ||
| - "workflow/**" | ||
| types: | ||
| - opened | ||
| # - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| - converted_to_draft | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| system-testing: | ||
| name: System testing - QuaC | ||
| runs-on: ubuntu-20.04 | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
|
|
||
| steps: | ||
| - name: Frees Disk Space (Ubuntu) | ||
| # For more info about this task, see https://github.com/uab-cgds-worthey/quac/issues/78 | ||
| uses: jlumbroso/free-disk-space@v1.2.0 | ||
| with: | ||
| # this might remove tools that are actually needed, when set to "true" | ||
| tool-cache: true | ||
|
|
||
| - name: Checkout repository | ||
| uses: actions/checkout@v2 | ||
|
|
||
| - name: Create quac environment | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| mamba-version: "*" | ||
| channels: conda-forge,bioconda,defaults | ||
| auto-activate-base: false | ||
| activate-environment: quac | ||
| environment-file: configs/env/quac.yaml | ||
|
|
||
| - name: Check conda solution | ||
| run: | | ||
| mamba env export | ||
| - name: Check snakemake exists in conda env | ||
| run: | | ||
| which snakemake | ||
| snakemake --version | ||
| - uses: eWaterCycle/setup-singularity@v7 | ||
| with: | ||
| singularity-version: 3.8.3 | ||
|
|
||
| - name: Check singularity is working | ||
| run: | | ||
| singularity --version | ||
| - name: Set up dependencies for QuaC | ||
| run: | | ||
| bash src/setup_dependency_datasets.sh | ||
| - name: Run QuaC system testing - WGS mode AND no prior QC data | ||
| run: | | ||
| PROJECT_CONFIG="project_2samples" | ||
| PRIOR_QC_STATUS="no_priorQC" | ||
| USE_SLURM="" | ||
| python src/run_quac.py \ | ||
| --project_name test_project \ | ||
| --projects_path ".test/ngs-data/" \ | ||
| --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \ | ||
| --outdir "data/quac/results/test_${PROJECT_CONFIG}_wgs-${PRIOR_QC_STATUS}/analysis" \ | ||
| --quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \ | ||
| --workflow_config "configs/workflow.yaml" \ | ||
| $USE_SLURM \ | ||
| || df -h | ||
| - name: Run QuaC system testing - Exome mode AND no prior QC data | ||
| run: | | ||
| PROJECT_CONFIG="project_2samples" | ||
| PRIOR_QC_STATUS="no_priorQC" | ||
| USE_SLURM="" | ||
| python src/run_quac.py \ | ||
| --project_name test_project \ | ||
| --projects_path ".test/ngs-data/" \ | ||
| --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \ | ||
| --outdir "data/quac/results/test_${PROJECT_CONFIG}_exome-${PRIOR_QC_STATUS}/analysis" \ | ||
| --quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \ | ||
| --workflow_config "configs/workflow.yaml" \ | ||
| --exome \ | ||
| $USE_SLURM \ | ||
| || df -h | ||
| - name: Run QuaC system testing - WGS mode AND uses prior QC data | ||
| run: | | ||
| PROJECT_CONFIG="project_2samples" | ||
| PRIOR_QC_STATUS="include_priorQC" | ||
| USE_SLURM="" | ||
| python src/run_quac.py \ | ||
| --project_name test_project \ | ||
| --projects_path ".test/ngs-data/" \ | ||
| --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \ | ||
| --outdir "data/quac/results/test_${PROJECT_CONFIG}_wgs-${PRIOR_QC_STATUS}/analysis" \ | ||
| --quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \ | ||
| --include_prior_qc \ | ||
| --allow_sample_renaming \ | ||
| --workflow_config "configs/workflow.yaml" \ | ||
| $USE_SLURM \ | ||
| || df -h | ||
| - name: Run QuaC system testing - Exome mode AND uses prior QC data | ||
| run: | | ||
| PROJECT_CONFIG="project_2samples" | ||
| PRIOR_QC_STATUS="include_priorQC" | ||
| USE_SLURM="" | ||
| python src/run_quac.py \ | ||
| --project_name test_project \ | ||
| --projects_path ".test/ngs-data/" \ | ||
| --pedigree ".test/configs/${PRIOR_QC_STATUS}/${PROJECT_CONFIG}.ped" \ | ||
| --outdir "data/quac/results/test_${PROJECT_CONFIG}_exome-${PRIOR_QC_STATUS}/analysis" \ | ||
| --quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \ | ||
| --exome \ | ||
| --include_prior_qc \ | ||
| --allow_sample_renaming \ | ||
| --workflow_config "configs/workflow.yaml" \ | ||
| $USE_SLURM \ | ||
| || df -h |
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