ci: testing through apptainer #38
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| name: Testing | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| jobs: | |
| Testing: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # --- FIX FOR DISK SPACE --- | |
| - name: Free Disk Space (Ubuntu) | |
| uses: jlumbroso/free-disk-space@main | |
| with: | |
| tool-cache: true | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| docker-images: true | |
| swap-storage: true | |
| - name: Checkout repository with submodules | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - name: Setup Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| apptainer-version: '1.2.5' | |
| - name: Prepare Test Data and Models | |
| run: | | |
| gzip -d .test/test_data/chr6_cdna.fa.gz | |
| gzip -d .test/test_data/genome_chr6.fa.gz | |
| mv .test/test_data/genome_chr6.fa.gz.fai .test/test_data/genome_chr6.fa.fai | |
| mkdir -p workflow/supplementary_res/deepvariant_rna_model | |
| BASE_URL="https://storage.googleapis.com/deepvariant/models/DeepVariant/1.4.0/DeepVariant-inception_v3-1.4.0+data-rnaseq_standard" | |
| wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.data-00000-of-00001" | |
| wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.example_info.json" | |
| wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.index" | |
| wget -q -P workflow/supplementary_res/deepvariant_rna_model "$BASE_URL/model.ckpt.meta" | |
| echo "Files in deepvariant_rna_model:" | |
| ls -l workflow/supplementary_res/deepvariant_rna_model/ | |
| - name: Test workflow | |
| uses: snakemake/snakemake-github-action@v1.22.0 | |
| env: | |
| APPTAINER_DISABLE_CACHE: "true" | |
| with: | |
| directory: .test | |
| snakefile: .test/Snakefile | |
| args: "--configfile .test/config/config.yaml --use-apptainer --show-failed-logs --cores 2" |