barcode update #255

	name: barcode update

	on:
	schedule:
	- cron: '0 0 * * *'

	jobs:
	testsuite:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash

	steps:
	- name: Check out repository code
	uses: actions/checkout@main
	with:
	repo-token: ${{ secrets.GITHUB_TOKEN }}

	- name: Setup for conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	channels: bioconda,conda-forge
	channel-priority: true
	python-version: 3.7
	activate-environment: test

	- name: Install
	shell: bash -l {0}
	run: \|
	conda install -n base conda-libmamba-solver
	conda config --set solver libmamba
	conda config --add channels bioconda
	conda config --add channels conda-forge
	conda install --yes --file ci/conda_requirements.txt
	pip install -e . --no-deps

	- name: update
	shell: bash -l {0}
	run: \|
	conda activate test
	freyja update --buildlocal

	- name: commit if output is different
	run: \|
	echo "running git diff, committing if different"
	if [[($(git status freyja/data/usher_barcodes.csv --porcelain \| wc -c) -ne 0)]]; then
	echo "changes were made, updating barcodes"
	git config --local user.name "$GITHUB_ACTOR"
	git config --local user.email "[email protected]"
	echo $(date +"%m_%d_%Y-%H-%M")> freyja/data/last_barcode_update.txt
	git add freyja/data/last_barcode_update.txt
	git add freyja/data/lineages.yml
	git add freyja/data/usher_barcodes.csv
	git add freyja/data/curated_lineages.json
	git commit -m "updating barcodes and metadata"
	git push origin main
	else
	echo "no changes were made, doing nothing."
	fi;

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