Add RNA-Seq TIN QC support #251

	# This workflow will build and test LongReadSum

	name: build tests

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	jobs:
	build-and-test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Download assets
	uses: dsaltares/[email protected]
	with:
	repo: 'WGLab/LongReadSum'
	version: 'tags/v1.3.1'
	file: 'SampleData.zip'

	- name: Unzip assets
	shell: bash --login {0}
	run: unzip SampleData.zip

	- name: Set up conda environment
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: longreadsum
	environment-file: environment.yml
	python-version: 3.9
	auto-activate-base: false

	- name: Check conda environment activation
	shell: bash --login {0}
	run: \|
	conda info --envs
	which python
	python --version
	conda list \| grep htslib
	conda list \| grep hdf5

	- name: Build LongReadSum
	shell: bash --login {0} # --login enables PATH variable access
	run: \|
	export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/share/miniconda/envs/longreadsum/lib
	conda info --envs
	which python
	python --version
	conda list \| grep htslib
	conda list \| grep hdf5
	ls /usr/share/miniconda/envs/longreadsum/lib \| grep hts
	ls /usr/share/miniconda/envs/longreadsum/lib \| grep hdf5
	make

	- name: Run tests
	shell: bash --login {0}
	run: \|
	mkdir output # Unit test output folder
	python -m pytest

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