updating to mip v12.1.0 #2695

	---

	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

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