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2862 fix determine base dir #2863

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merged 3 commits into from
Mar 19, 2024
Merged

2862 fix determine base dir #2863

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820510f
Fix the check for base dir to ensure we check if the supplied dir has…
awgymer Mar 18, 2024
fe8cdfb
Merge branch 'dev' into 2862-fix-determine-base-dir
ewels Mar 19, 2024
68ab4fe
Update CHANGELOG
awgymer Mar 19, 2024
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7 changes: 4 additions & 3 deletions nf_core/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1047,12 +1047,13 @@ def load_tools_config(directory: Union[str, Path] = "."):

def determine_base_dir(directory="."):
base_dir = start_dir = Path(directory).absolute()
while base_dir != base_dir.parent:
# Only iterate up the tree if the start dir doesn't have a config
while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent:
base_dir = base_dir.parent
config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
if config_fn:
return directory if base_dir == start_dir else base_dir
return directory
break
return directory if base_dir == start_dir else base_dir


def get_first_available_path(directory, paths):
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