Update automated_tests.yml based on .gitlab-ci.yml #56

	name: Automated tests

	on: [push]

	jobs:
	test:
	runs-on: ubuntu-20.04

	steps:
	- uses: actions/checkout@v2
	with:
	submodules: 'true'
	- name: Install dependencies
	run: \|
	# install system dependencies
	apt-get --quiet update && apt-get --quiet --assume-yes install curl unzip zip wget make tree
	# install SDKMAN as SDK version manager
	curl -s "https://get.sdkman.io?rcupdate=false" \| bash
	source "/root/.sdkman/bin/sdkman-init.sh"
	sdk version
	# install java (amazon coretto release 17.0.6)
	sdk install java 17.0.6-amzn
	java -version
	# install nextflow
	wget -qO- https://get.nextflow.io \| bash && mv nextflow /usr/local/bin/
	which nextflow
	# install mamba
	wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
	mkdir /root/.conda
	bash Mambaforge-Linux-x86_64.sh -b -p /usr/local/bin/conda
	rm -f Mambaforge-Linux-x86_64.sh
	source /usr/local/bin/conda/etc/profile.d/conda.sh
	source /usr/local/bin/conda/etc/profile.d/mamba.sh
	which mamba
	mamba --version
	# this is a workaround for https://github.com/mamba-org/mamba/issues/1993
	echo "use_lockfiles:" >> ~/.condarc
	echo " - false" >> ~/.condarc
	echo "channels:" >> ~/.condarc
	echo " - defaults" >> ~/.condarc
	echo " - conda-forge" >> ~/.condarc
	echo " - bioconda" >> ~/.condarc
	cat ~/.condarc
	#- name: Cache conda environments
	# uses: actions/cache@v2
	# with:
	# path: \|
	# /home/runner/work/tronflow-cnvkit/tronflow-cnvkit/work/conda
	# key: ${{ runner.os }}-tronflow-cnvkit
	- name: Run tests
	run: \|
	export PATH="/usr/local/bin/conda/bin:${PATH}"
	echo $PATH
	make

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