Modules: patch: handle file not found when it is an added file to a module #6329

Job	Run time
Get test file matrix	3s
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 3.11 on ubuntu-latest	49s
Run test_test_utils.py with Python 3.11 on ubuntu-latest	40s
Run test_sync.py with Python 3.11 on ubuntu-latest	56s
Run test_subworkflows.py with Python 3.11 on ubuntu-latest	5m 28s
Run test_schema.py with Python 3.11 on ubuntu-latest	1m 16s
Run test_refgenie.py with Python 3.11 on ubuntu-latest	49s
Run test_params_file.py with Python 3.11 on ubuntu-latest	42s
Run test_modules.py with Python 3.11 on ubuntu-latest	4m 45s
Run test_list.py with Python 3.11 on ubuntu-latest	48s
Run test_lint_utils.py with Python 3.11 on ubuntu-latest	47s
Run test_lint.py with Python 3.11 on ubuntu-latest	2m 4s
Run test_licenses.py with Python 3.11 on ubuntu-latest	40s
Run test_launch.py with Python 3.11 on ubuntu-latest	1m 17s
Run test_download.py with Python 3.11 on ubuntu-latest	1m 21s
Run test_create_logo.py with Python 3.11 on ubuntu-latest	41s
Run test_create.py with Python 3.11 on ubuntu-latest	1m 2s
Run test_components.py with Python 3.11 on ubuntu-latest	9m 11s
Run test_cli.py with Python 3.11 on ubuntu-latest	40s
Run test_bump_version.py with Python 3.11 on ubuntu-latest	49s
coverage	47s
	35m 38s

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