feat: Varscan2 - SnpEff Meta wrapper #6103

	name: Code quality

	on:
	pull_request:
	branches_ignore: []

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Setup mamba
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: fmt
	channels: "conda-forge, bioconda"
	miniforge-version: latest

	- name: Setup environment
	shell: bash -el {0}
	run: \|
	conda config --set channel_priority strict
	conda install -n fmt -y black snakefmt

	- name: Check Python formatting
	shell: bash -el {0}
	run: \|
	black --check ///wrapper.py /*/wrapper.py

	# TODO reactivate once comment errors are fixed
	# - name: Check Snakemake formatting
	# run: \|
	# export PATH="/usr/share/miniconda/bin:$PATH"
	# source activate fmt
	# snakefmt --check $(git diff origin/master --name-only \| grep Snakefile)

	linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v1

	- name: Setup mamba
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: snakemake
	channels: "conda-forge, bioconda"
	miniforge-version: latest

	- name: Setup Snakemake environment
	shell: bash -el {0}
	run: \|
	conda config --set channel_priority strict
	conda install -n snakemake -y snakemake-minimal snakemake

	- name: Fetch master
	run: \|
	git fetch origin master

	- name: Linting
	shell: bash -el {0}
	run: \|
	declare -i ERRORS=0
	# get all modified and added files, not those that are deleted
	for f in $(git diff origin/master --name-only --diff-filter=d \| grep Snakefile)
	do
	snakemake -s $f --lint
	ERRORS+=$?
	done
	if (( $ERRORS > 0 ))
	then
	echo "There are some lints above. Please fix them."
	exit 1
	fi

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