Run pipeline #163

	name: Run pipeline
	on:
	workflow_dispatch:
	repository_dispatch:
	types: [run_pipeline]
	schedule:
	- cron: '20 0 * * 0,3'

	jobs:
	update-file:
	runs-on: ubuntu-20.04
	steps:
	- name: checkout
	uses: actions/checkout@v3
	with:
	fetch-depth: 0
	ref: master
	- name: Install Python
	uses: actions/setup-python@v1
	with:
	python-version: 3.9
	- name: Install python dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install subversion -y
	python -m pip install --upgrade pip
	pip install poetry
	poetry config virtualenvs.create false
	poetry install --no-dev
	- name: Install and set up transvar
	run: \|
	. transvar_env_vars.sh
	sudo apt install -y samtools tabix
	bash set_up_transvar.sh
	- name: Update file
	run: \|
	. transvar_env_vars.sh
	bash run_analysis.sh
	- name: Commit changes
	uses: stefanzweifel/git-auto-commit-action@v4
	with:
	commit_message: updated to last revision
	file_pattern: ".tsv .json .contig genome.pickle"

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