test run_dataset mode for R tools #6
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| name: test run_dataset mode for R tools | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: [pull_request, workflow_dispatch ] | |
| jobs: | |
| run_dataset: | |
| name: Run workflow with run_dataset mode | |
| 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 pipeline with test data | |
| run: | | |
| nextflow run main.nf -profile test,docker --mode run_dataset \ | |
| --methods rctd,music,spatialdwls,nnls,seurat | |
| - name: Upload proportions and metrics | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: deconv-proportions-and-metrics | |
| path: | | |
| deconv_proportions/* | |
| results/* | |
| trace.txt | |
| test_output_run_dataset: | |
| name: Tests outputs of the pipeline | |
| needs: run_dataset | |
| runs-on: ubuntu-latest | |
| container: rocker/tidyverse:3.6.3 | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Download proportions from test run | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: deconv-proportions-and-metrics | |
| - name: Check proportions and metrics with testthat | |
| shell: bash | |
| run: | | |
| echo $(ls) | |
| Rscript unit-test/test_run_dataset.R \ | |
| rctd,music,spatialdwls |