Merge pull request #30 from clinical-genomics-uppsala/fix_at_first_cl… #35

	name: small integration test

	# Controls when the action will run.
	on:
	# Triggers the workflow on push or pull request events but only for the master and develop branch
	push:
	branches:
	- develop
	- main

	# Allows you to run this workflow manually from the Actions tab
	workflow_dispatch:

	jobs:
	integration-small-singularity:
	name: integration small data set singularity
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.8
	uses: actions/setup-python@v3
	with:
	python-version: 3.8
	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	activate-environment: my-env
	use-mamba: true
	- name: Set strict channels
	run: \|
	conda config --set channel_priority strict
	- name: Install requirements.txt
	run: \|
	pip install -r requirements.txt
	- name: Install requirements.test.txt
	run: \|
	pip install -r requirements.test.txt
	- name: Install singularity
	run: \|
	mamba install -c conda-forge -c bioconda singularity=3.8.6
	- name: Add conda to system path
	run: \|
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Integration test - small dataset
	working-directory: .tests/integration
	run: \|
	snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs --configfiles ../../config/config.yaml config.yaml --config sequenceid="test" --use-singularity --singularity-args " --cleanenv --bind /home/runner "

Provide feedback