test_run_dataset_R.yml

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
        shell: bash
        run: |
          nextflow run main.nf -profile test,docker --mode run_dataset \
          --methods rctd,music,spatialdwls,nnls,seurat
          echo $(ls)

      - 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