Merge pull request #2067 from Clinical-Genomics/update_clinvar_loqusdb #2826

	---

	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

Provide feedback