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Validation of meta.yaml in cross-org repos #3680

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58c431d
Use the repo's own JSON files rather than the central ones
muffato Jul 15, 2025
3df3003
With cross-org repos, components can be dictionaries whose (only) key…
muffato Jul 15, 2025
6b80db2
[automated] Update CHANGELOG.md
nf-core-bot Jul 15, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,7 @@
### General

- don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))
- Validation of meta.yaml in cross-org repos ([#3680](https://github.com/nf-core/tools/pull/3680))

## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]

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2 changes: 1 addition & 1 deletion nf_core/modules/lint/meta_yml.py
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Expand Up @@ -72,7 +72,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
# Confirm that the meta.yml file is valid according to the JSON schema
valid_meta_yml = False
try:
with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/meta-schema.json")) as fh:
with open(Path(module.base_dir, "modules/meta-schema.json")) as fh:
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I am not sure we should change this. module_lint_object.modules_repo.local_repo_dir is checking the cloned modules repository, which should be the one that is being used.
I think what should be changed is the repo that we are cloning to the cache. I was trying to make some test with the test modules repo but there seems to be an error, my suggestion would be to fix that repo until it is useable and then we can figure out the best way to adapt it.

schema = json.load(fh)
validators.validate(instance=meta_yaml, schema=schema)
module.passed.append(("meta_yml_valid", "Module `meta.yml` is valid", module.meta_yml))
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4 changes: 2 additions & 2 deletions nf_core/subworkflows/lint/meta_yml.py
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Expand Up @@ -53,7 +53,7 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
# Confirm that the meta.yml file is valid according to the JSON schema
valid_meta_yml = True
try:
with open(Path(subworkflow_lint_object.modules_repo.local_repo_dir, "subworkflows/yaml-schema.json")) as fh:
with open(Path(subworkflow.base_dir, "subworkflows/yaml-schema.json")) as fh:
schema = json.load(fh)
jsonschema.validators.validate(instance=meta_yaml, schema=schema)
subworkflow.passed.append(("meta_yml_valid", "Subworkflow `meta.yml` is valid", subworkflow.meta_yml))
Expand Down Expand Up @@ -115,7 +115,7 @@ def meta_yml(subworkflow_lint_object, subworkflow, allow_missing: bool = False):
# join included modules and included subworkflows in a single list
included_components_names = [component["name"] for component in included_components]
if "components" in meta_yaml:
meta_components = [x for x in meta_yaml["components"]]
meta_components = [x if isinstance(x, str) else list(x)[0] for x in meta_yaml["components"]]
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this change looks good 🙂

for component in set(included_components_names):
if component in meta_components:
subworkflow.passed.append(
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