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Fix linting fail on nfcore_external_java_deps if nf_schema is used #2976

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merged 6 commits into from
May 13, 2024
Merged

Fix linting fail on nfcore_external_java_deps if nf_schema is used #2976

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671e1df
Merge pull request #2958 from nf-core/dev
mashehu May 8, 2024
930ece5
Merge pull request #2971 from nf-core/dev
mashehu May 9, 2024
3cf57a8
Added nf-schema as condition to exclude Java deps file
itrujnara May 10, 2024
0bdd4dd
add explicit test for nf-schema
mashehu May 10, 2024
05cb3f2
Merge branch 'dev' into fix_deps_lint_nf_schema
mashehu May 10, 2024
c3e2844
[automated] Update CHANGELOG.md
nf-core-bot May 10, 2024
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13 changes: 7 additions & 6 deletions nf_core/lint/files_exist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,8 +200,8 @@ def files_exist(self) -> Dict[str, Union[List[str], bool]]:
Path("Singularity"),
]
files_warn_ifexists = [Path(".travis.yml")]
files_fail_ifinconfig: List[Tuple[Path, Dict[str, str]]] = [
(Path("lib", "nfcore_external_java_deps.jar"), {"plugins": "nf-validation"}),
files_fail_ifinconfig: List[Tuple[Path, List[Dict[str, str]]]] = [
(Path("lib", "nfcore_external_java_deps.jar"), [{"plugins": "nf-validation"}, {"plugins": "nf-schema"}]),
]

# Remove files that should be ignored according to the linting config
Expand Down Expand Up @@ -246,10 +246,11 @@ def pf(file_path: Union[str, Path]) -> Path:
if str(file_cond[0]) in ignore_files:
continue
in_config = False
config_key, config_value = list(file_cond[1].items())[0]
if config_key in self.nf_config and config_value in self.nf_config[config_key]:
log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
in_config = True
for condition in file_cond[1]:
config_key, config_value = list(condition.items())[0]
if config_key in self.nf_config and config_value in self.nf_config[config_key]:
log.debug(f"Found {config_key} in nextflow.config with value {config_value}")
in_config = True
if pf(file_cond[0]).is_file() and in_config:
failed.append(f"File must be removed: {self._wrap_quotes(file_cond[0])}")
elif pf(file_cond[0]).is_file() and not in_config:
Expand Down
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