Apptainer Run #54


	name: Apptainer Run

	on:
	push:
	branches:
	- main
	- dev
	pull_request:
	branches-ignore: []
	schedule:
	- cron: '0 0 15 * *'

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	matrix:
	# py3.9 fails
	python: [ 3.8, '3.10']
	fail-fast: false


	steps:

	- name: install graphviz
	run: \|
	sudo apt-get install -y graphviz

	- name: checkout git repo
	uses: actions/checkout@v2

	- name: Set up Python 3.X
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python }}

	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH

	- name: conda
	run: \|
	conda install -c conda-forge -c bioconda --quiet -y python=${{ matrix.python }} 'singularity>3'

	- name: Install dependencies
	run: \|
	pip install .[testing]

	- name: install package itself
	run: \|
	pip install .

	- name: testing
	run: \|
	sequana_nanomerge --input-directory test/data/barcoded --sample-sheet test/data/samplesheet.csv --input-pattern "barcode/fastq.gz" --summary test/data/sequence_summary.txt --use-apptainer && cd nanomerge && sh nanomerge.sh

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