test data generation #12
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| name: test data generation | |
| # This workflow generates synthetic data | |
| on: [pull_request, workflow_dispatch] | |
| jobs: | |
| generate_data: | |
| name: Run workflow to generate synthetic data | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Nextflow versions: check pipeline minimum and latest edge version | |
| nxf_ver: | |
| - 'NXF_VER=21.04.3' | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| # with: | |
| # lfs: true | |
| - name: Download test dataset | |
| run: | | |
| wget https://zenodo.org/record/5763377/files/test_data.tar.gz?download=1 -O test_data.tar.gz | |
| tar -xzvf test_data.tar.gz | |
| echo $(ls) | |
| # - name: Checkout LFS objects | |
| # run: git lfs checkout | |
| - name: Install Nextflow | |
| run: | | |
| wget -qO- get.nextflow.io | bash | |
| sudo mv nextflow /usr/local/bin/ | |
| export ${{ matrix.nxf_ver }} | |
| nextflow self-update | |
| - name: Run data generation script | |
| run: | | |
| nextflow run subworkflows/data_generation/generate_data.nf -profile test,docker | |
| - name: Check output files | |
| run: | | |
| echo ">>> Checking if all synthetic datasets are generated" | |
| if [ `ls -1 synthetic_data/*.rds | wc -l` -ne 6 ]; then exit 1; fi | |
| echo ">>> Checking file names" | |
| for REP in rep1 rep2; do | |
| for DATASET_TYPE in artificial_diverse_distinct artificial_uniform_distinct prior_from_data; do | |
| if [ ! -f "synthetic_data/test_sc_data_${DATASET_TYPE}_${REP}.rds" ] | |
| then exit 1; fi ; done; done | |
| - name: Upload synthetic data | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: synthetic-data | |
| path: | | |
| synthetic_data/test_sc_data_artificial_diverse_distinct_rep1.rds | |
| test_output_generate: | |
| name: Tests outputs of the pipeline | |
| needs: generate_data | |
| runs-on: ubuntu-latest | |
| container: rocker/tidyverse:3.6.3 | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Download generated synthetic data | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: synthetic-data | |
| - name: Check synethic data structure | |
| shell: bash | |
| run: | | |
| echo $(ls) | |
| Rscript unit-test/test_generate_data.R test_sc_data_artificial_diverse_distinct_rep1.rds |