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MIP CI tests

adding documentation #2805

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adding documentation

adding documentation #2805

Workflow file for this run

.github/workflows/testing.yml at 29217b0
---
name: MIP CI tests
"on": ["pull_request", "push"]
jobs:
tests:
name: MIP test suite
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: shogo82148/actions-setup-perl@v1
with:
perl-version: '5.26'
- uses: conda-incubator/setup-miniconda@v2
with:
channels: bioconda, conda-forge
- name: Set up perl
run: |
perl -V
cpanm --quiet --notest --installdeps .
- name: Install bcftools in conda test env
shell: bash -l {0}
run: |
conda create -n mip_ci --channel bioconda --channel conda-forge bcftools=1.9=ha228f0b_4
- name: Run MIP install test
shell: bash -l {0}
run: perl t/mip_install.test
- name: Install MIP rare disease
shell: bash -l {0}
run: |
perl mip install --envn mip_ci --select_program mip_scripts
- 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