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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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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
- Update python:3.11-slim Docker digest to a2eb07f ([#2847](https://github.com/nf-core/tools/pull/2847))
- Strip out mention of "Nextflow Tower" and replace with "Seqera Platform" wherever possible
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.3 ([#2850](https://github.com/nf-core/tools/pull/2850))
- Fix issue with config resolution that was causing nested configs to behave unexpectedly ([#2862](https://github.com/nf-core/tools/pull/2862))

## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

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7 changes: 4 additions & 3 deletions nf_core/utils.py
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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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