fix: update Snakemake command to use Singularity instead of Docker #16

	name: Test GHCR Container

	on:
	push:
	pull_request:

	jobs:
	test-container:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Pull container presto-0.7.4:latest from GHCR
	run: \|
	docker pull ghcr.io/lewisl23/presto-0.7.4:latest

	- name: Test container presto-0.7.4:latest runs
	run: \|
	docker run --rm ghcr.io/lewisl23/presto-0.7.4:latest AssemblePairs.py --help
	echo "Container works"

	- name: Pull container igblast-1.21.0:latest from GHCR
	run: \|
	docker pull ghcr.io/lewisl23/igblast-1.21.0:latest

	- name: Test container igblast-1.21.0:latest runs
	run: \|
	docker run --rm ghcr.io/lewisl23/igblast-1.21.0:latest igblastn -help
	echo "Container works"

	test-workflow:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.9"

Check failure on line 44 in .github/workflows/main.yml View workflow run for this annotation GitHub Actions / .github/workflows/main.yml Invalid workflow file `You have an error in your yaml syntax on line 44`
	- name: Install Snakemake
	run: \|
	pip install snakemake
	pip install pulp==2.7.0

	- name: Install Apptainer
	run: \|
	sudo apt-get update
	sudo apt-get install -y apptainer

	- name: Run test pipeline
	run: \|
	snakemake --cores 1 \
	--configfile tests/config/test_config.yaml \
	--use-singularity \
	--printshellcmds \
	--reason \
	all

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