EVA-3330: Add labels to nextflow for SLURM migration #149

	name: Variant Remapping

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.8]

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	# Install dependencies
	sudo apt-get install libgsl0-dev
	# Install Nextflow
	mkdir /tmp/nextflow && cd /tmp/nextflow
	wget -qO- get.nextflow.io \| bash
	echo "/tmp/nextflow" >> $GITHUB_PATH
	cd -
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	$CONDA/bin/conda update conda # https://github.com/conda/conda/issues/13560
	$CONDA/bin/conda install -y python=${{ matrix.python-version }} # https://github.com/actions/setup-python/issues/833
	$CONDA/bin/conda env update -q --file conda.yml --name base
	$CONDA/bin/conda run pip install -q -r requirements.txt

	- name: Test nextflow workflow
	run: \|
	$CONDA/bin/conda run tests/test_pipeline.sh
	$CONDA/bin/conda run tests/test_pipeline_empty.sh

	- name: Test with pytest
	run:
	$CONDA/bin/conda run PYTHONPATH=. pytest variant_remapping_tools/tests

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