Add a selectgenotype switch to selectvariants #16

	name: Continuous Integration

	on: [push, pull_request]

	defaults:
	run:
	# This is needed for miniconda, see:
	# https://github.com/marketplace/actions/setup-miniconda#important.
	shell: bash -l {0}

	jobs:
	test:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	test:
	- womtool-malesample
	- womtool-multisample-fallback
	- malesample
	- two-samples
	- two-samples-fallback
	- no-samplenameVcf
	steps:
	- uses: actions/[email protected] # https://github.com/actions/checkout.
	with:
	submodules: recursive
	- name: Install miniconda
	uses: conda-incubator/[email protected] # https://github.com/conda-incubator/setup-miniconda.
	with:
	channels: conda-forge,bioconda,defaults
	- name: Install requirements.
	run: conda install -n test --file requirements-test.txt
	- name: Run test in conda environment
	# Use --symlink to limit disk usage.
	run: >-
	pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }}
	--symlink tests/
	- name: Check cromwell log in case of failure.
	if: ${{ failure() }}
	# Get the last 1000 lines of the cromwell log to catch the error.
	run: bash -c 'tail -n 1000 /tmp/pytest_workflow_//log.out'
	- name: Check job stderr messages in case of failure
	if: ${{ failure() }}
	run: >-
	bash -c '
	for file in $(find /tmp -name stderr);
	do echo $file; cat $file; done'
	- name: Check job stdout messages in case of failure
	if: ${{ failure() }}
	run: >-
	bash -c '
	for file in $(find /tmp -name stdout);
	do echo $file; cat $file; done'

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