shm and se changes #529

	name: Sequence Processing Pipeline CI

	# Controls when the action will run.
	on:
	# Triggers the workflow on pull request and push events, only on the master
	# branch
	pull_request:
	branches: [ master ]
	push:
	branches: [ master ]

	jobs:
	# name of job
	build:
	# The type of runner that the job will run on (available options are window/macOS/linux)
	runs-on: ubuntu-latest
	# we can add more versions of node.js in the future
	strategy:
	matrix:
	python-version: ['3.9']

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	# first grab branch from github
	- uses: actions/checkout@v2
	with:
	persist-credentials: false
	fetch-depth: 0

	- uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: tester
	python-version: ${{ matrix.python-version }}
	conda-channels: anaconda, conda-forge, bioconda
	auto-update-conda: true

	- name: Main install
	shell: bash -l {0}
	run: \|
	conda install bioconda::fastq-pair
	pip install -e ".[all]"

	- name: Python linter
	shell: bash -l {0}
	run: flake8 sequence_processing_pipeline/ setup.py

	- name: Run tests and measure coverage
	shell: bash -l {0}
	run: \|
	nosetests --with-coverage --cover-inclusive --cover-package sequence_processing_pipeline

	- name: Coveralls
	uses: AndreMiras/coveralls-python-action@develop
	with:
	parallel: true
	flag-name: Unit Test

	coveralls_finish:
	needs: build
	runs-on: ubuntu-latest
	steps:
	- name: Coveralls Finished
	uses: AndreMiras/coveralls-python-action@develop
	with:
	github-token: ${{ secrets.github_token }}
	parallel-finished: true

Provide feedback