Issue 391 - Updates to EFO feedback processing #346

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: CMAT pipelines

	on:
	pull_request:
	branches: [ master ]
	workflow_dispatch:


	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8
	- name: Install native packages
	run: \|
	sudo apt update
	sudo apt -y install samtools bcftools parallel libbz2-dev liblzma-dev
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	python setup.py install
	- name: Install Nextflow
	run: \|
	mkdir /tmp/nextflow && cd /tmp/nextflow
	wget -qO- get.nextflow.io \| bash
	echo "/tmp/nextflow" >> $GITHUB_PATH
	cd -

	- name: Unit tests
	run: python -m pytest --cov=cmat -k "not integration"

	- name: Integration tests
	run: python -m pytest --cov=cmat --cov-append tests -k integration

	- name: End-to-end test of evidence string generation pipeline
	run: bash tests/pipelines/test_annotation_pipeline.sh

	# TODO Takes too long to run regularly, maybe just on tags?
	# - name: End-to-end test of curation pipelines
	# run: bash tests/pipelines/test_curation_pipelines.sh

	- name: Upload the coverage data to Coveralls
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: coveralls

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