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don't read param expressions with spaces as params #3674

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Merged
mirpedrol merged 3 commits into from
Jul 15, 2025
Merged

don't read param expressions with spaces as params #3674

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ef427b5
don't read param expressions with spaces as params
mirpedrol Jul 10, 2025
bb13b04
[automated] Update CHANGELOG.md
nf-core-bot Jul 10, 2025
587b816
add test for fetch_wf_config utils
mirpedrol Jul 10, 2025
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don't read param expressions with spaces as params
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@mirpedrol
mirpedrol committed Jul 10, 2025
commit ef427b5dd263e3ce5990517ff4c8384d6dd578e3
2 changes: 1 addition & 1 deletion nf_core/utils.py
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Expand Up @@ -326,7 +326,7 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict:
if result is not None:
nfconfig_raw, _ = result
nfconfig = nfconfig_raw.decode("utf-8")
multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL)
multiline_key_value_pattern = re.compile(r"(^|\n)([^\n=\s]+?)\s*=\s*((?:(?!\n[^\n=]+?\s*=).)*)", re.DOTALL)

for config_match in multiline_key_value_pattern.finditer(nfconfig):
k = config_match.group(2).strip()
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