put symlinks in an indir #92

	name: denv_pipeline
	on: [push, pull_request]
	defaults:
	run:
	shell: bash -el {0}

	jobs:
	run_pipeline_tests:
	name: analysis_pipeline test on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ["ubuntu-latest", "macos-latest"]
	steps:
	- uses: actions/checkout@v2
	- uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: environment.yml
	activate-environment: analysis_env
	channels: conda-forge,bioconda,defaults
	conda-version: "*"
	- name: install pipeline
	run: pip install -e .
	- name: run_dry_run
	working-directory: tests
	run: denv_pipeline --config dry_run_config.yml --dry-run
	- name: test_setup
	working-directory: tests
	run: python scripts/unit_tests_dry_run.py
	\--in-config dry_run_config.yml
	\--out-config test_output_dry_run/output_config.yml
	\--outdir test_output_dry_run
	- name: install snakemake dependencies
	run: python -m pip install --upgrade pip pandas
	- name: run_full
	working-directory: tests
	run: denv_pipeline --config base_run_config.yml

	- name: test_results
	working-directory: tests
	run: python scripts/unit_tests_results.py
	\--outdir test_output_full_run/results
	\--depth 10

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