conda_prod_install.yml

---

name: MIP CI conda production install

"on": ["pull_request", "push"]

jobs:
  tests:
    name: MIP production install
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: conda-incubator/setup-miniconda@v2
        with:
          channels: bioconda, conda-forge

      - name: Set up perl using conda
        shell: bash -l {0}
        run: |
          bash mip_install_perl.sh -e mip_ci -p /usr/share/miniconda

      - name: Run MIP install test
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          perl t/mip_install.test

      - name: Install MIP rare disease
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          perl mip install --envn mip_ci --select_program mip_scripts

      - name: Install bcftools in conda test env
        shell: bash -l {0}
        run: |
          conda install -n mip_ci --channel bioconda --channel conda-forge bcftools=1.9=ha228f0b_4

      - name: Run MIP unit tests
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          prove -lrs -f -j 2 t

      - name: Run MIP download test
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          perl t/mip_download.test

      - name: Run MIP analyse tests
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          perl t/mip_analyse_dragen_rd_dna.test
          perl t/mip_analyse_rd_dna_panel.test
          perl t/mip_analyse_rd_dna.test
          perl t/mip_analyse_rd_dna_vcf_rerun.test
          perl t/mip_analyse_rd_rna.test

      - name: Run MIP scripts tests
        shell: bash -l {0}
        run: |
          conda activate mip_ci
          perl t/mip_qccollect.test
          perl t/mip_vcfparser.test