oops pip typo #437

	name: Python Package using Conda

	on: [push]

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python 3.8
	uses: actions/setup-python@v2
	with:
	python-version: 3.8
	- 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: Install dependencies
	run: \|
	# conda env update --file covid1.1_environment.yml --name base
	conda install numpy=1.21.2
	conda install boto3
	# conda install wand -c conda-forge
	# conda install -c bioconda fastqc
	conda install -c bioconda qualimap
	conda install -c bioconda minimap2
	conda install -c bioconda samtools
	pip install multiqc
	pip install nwalign3
	pip install pandas==1.4.1
	# pip install seaborn
	pip install fastaparser
	- name: Lint with flake8
	run: \|
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# The GitHub editor is 127 chars wide
	flake8 . --count --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	run: \|
	conda install pytest
	pytest

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