Add files via upload #10

	name: Test Pipeline Components

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]

	jobs:
	test:
	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -l {0}

	steps:
	- uses: actions/checkout@v3

	- name: Set up Conda
	uses: conda-actions/setup-conda@v2
	with:
	python-version: '3.10'

	- name: Cache Conda env
	uses: actions/cache@v3
	with:
	path: \|
	/usr/share/miniconda/envs/
	key: conda-${{ hashFiles('environment.yml') }}
	restore-keys: \|
	conda-

	- name: Create Conda environment
	run: conda env create -f environment.yml

	- name: Run syntax checks
	run: \|
	conda activate taxonomy-pipeline

	# Check Perl scripts syntax
	echo "Checking Perl scripts syntax..."
	for script in workflow/scripts/*.pl; do
	echo "Checking $script"
	perl -cw $script
	done

	# Run Perl::Critic on scripts
	echo "Running Perl::Critic..."
	for script in workflow/scripts/*.pl; do
	echo "Analyzing $script"
	perlcritic --gentle $script
	done

	# Validate Snakefile syntax
	echo "Checking Snakefile syntax..."
	snakemake --lint

	# Test Snakemake dry run with minimal test data
	echo "Testing Snakefile dry run..."
	snakemake -n

	- name: Run unit tests
	run: \|
	conda activate taxonomy-pipeline
	cd tests
	prove -v *.t

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