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Fix bug with creating .nf-core.yml file when it can't be found #2562

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merged 4 commits into from
Dec 14, 2023
Merged

Fix bug with creating .nf-core.yml file when it can't be found #2562

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42f927b
fixed determine_base_dir so that that it works when no yaml is found
krokicki Dec 7, 2023
4308657
update changelog
krokicki Dec 8, 2023
8300cff
Merge branch 'dev' into allow_no_yaml
krokicki Dec 8, 2023
9f5a7d8
Merge branch 'dev' into allow_no_yaml
mirpedrol Dec 14, 2023
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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 @@ -29,6 +29,7 @@
- Replace ModulePatch by ComponentPatch ([#2482](https://github.com/nf-core/tools/pull/2482))
- Fixed `nf-core modules lint` to work with new module structure for nf-test ([#2494](https://github.com/nf-core/tools/pull/2494))
- Add option `--migrate-pytest` to create a module with nf-test taking into account an existing module ([#2549](https://github.com/nf-core/tools/pull/2549))
- When `.nf-core.yml` is not found create it in the current directory instead of the root filesystem ([#2237](https://github.com/nf-core/tools/issues/2237))
- Modules `--migrate-pytest` copies template scripts ([#2568](https://github.com/nf-core/tools/pull/2568))

### Subworkflows
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6 changes: 3 additions & 3 deletions nf_core/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1037,12 +1037,12 @@ def load_tools_config(directory: Union[str, Path] = "."):

def determine_base_dir(directory="."):
base_dir = start_dir = Path(directory).absolute()
while not get_first_available_path(base_dir, CONFIG_PATHS) and base_dir != base_dir.parent:
while base_dir != base_dir.parent:
base_dir = base_dir.parent
config_fn = get_first_available_path(base_dir, CONFIG_PATHS)
if config_fn:
break
return directory if base_dir == start_dir else base_dir
return directory if base_dir == start_dir else base_dir
return directory


def get_first_available_path(directory, paths):
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