one more regexp fix #2674
Workflow file for this run
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--- | |
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 |