Fix/remove deprecated linters #6406

Job	Run time
Get test file matrix	2s
setup (3.8, ubuntu-latest)	1s
setup (3.11, ubuntu-latest)	1s
setup (3.8, ubuntu-20.04)	1s
Run test_utils.py with Python 3.8 on ubuntu-latest	54s
Run test_test_utils.py with Python 3.8 on ubuntu-latest	47s
Run test_sync.py with Python 3.8 on ubuntu-latest	1m 8s
Run test_subworkflows.py with Python 3.8 on ubuntu-latest	6m 21s
Run test_schema.py with Python 3.8 on ubuntu-latest	1m 11s
Run test_refgenie.py with Python 3.8 on ubuntu-latest	1m 19s
Run test_params_file.py with Python 3.8 on ubuntu-latest	50s
Run test_modules.py with Python 3.8 on ubuntu-latest	4m 42s
Run test_list.py with Python 3.8 on ubuntu-latest	1m 1s
Run test_lint_utils.py with Python 3.8 on ubuntu-latest	48s
Run test_lint.py with Python 3.8 on ubuntu-latest	1m 54s
Run test_licenses.py with Python 3.8 on ubuntu-latest	58s
Run test_launch.py with Python 3.8 on ubuntu-latest	1m 16s
Run test_download.py with Python 3.8 on ubuntu-latest	1m 5s
Run test_create_logo.py with Python 3.8 on ubuntu-latest	48s
Run test_create.py with Python 3.8 on ubuntu-latest	57s
Run test_components.py with Python 3.8 on ubuntu-latest	10m 22s
Run test_cli.py with Python 3.8 on ubuntu-latest	56s
Run test_bump_version.py with Python 3.8 on ubuntu-latest	54s
coverage	54s
	39m 10s

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