def lint(self):
"""Perform linting on this module"""
# Iterate over modules and run all checks on them
# Lint the main.nf file
self.lint_main_nf()
# Lint the meta.yml file
self.lint_meta_yml()
# Lint the functions.nf file
self.lint_functions_nf()
# Lint the tests
if self.repo_type == "modules":
self.lint_module_tests()
# Check for TODOs
self.wf_path = self.module_dir
module_todos = pipeline_todos(self)
for i, warning in enumerate(module_todos["warned"]):
self.warned.append(
("module_todo", warning, module_todos["file_paths"][i]))
return self.passed, self.warned, self.failed
def module_todos(module_lint_object, module):
"""
Look for TODO statements in the module files
The nf-core module template contains a number of comment lines to help developers
of new modules know where they need to edit files and add content.
They typically have the following format:
.. code-block:: groovy
// TODO nf-core: Make some kind of change to the workflow here
..or in markdown:
.. code-block:: html
<!-- TODO nf-core: Add some detail to the docs here -->
This lint test runs through all files in the module and searches for these lines.
If any are found they will throw a warning.
.. tip:: Note that many GUI code editors have plugins to list all instances of *TODO*
in a given project directory. This is a very quick and convenient way to get
started on your pipeline!
"""
# Main module directory
mod_results = pipeline_todos(None, root_dir=module.module_dir)
for i, warning in enumerate(mod_results["warned"]):
module.warned.append(
("module_todo", warning, mod_results["file_paths"][i]))
for i, passed in enumerate(mod_results["passed"]):
module.passed.append(("module_todo", passed, module.module_dir))
# Module tests directory
test_results = pipeline_todos(None, root_dir=module.test_dir)
for i, warning in enumerate(test_results["warned"]):
module.warned.append(
("module_todo", warning, test_results["file_paths"][i]))
for i, passed in enumerate(test_results["passed"]):
module.passed.append(("module_todo", passed, module.test_dir))
def module_todos(module_lint_object, module):
"""
Look for TODO statements in the module files
Slight modification of the "nf_core.lint.pipeline_todos" function to make it work
for a single module
"""
module.wf_path = module.module_dir
results = pipeline_todos(module)
for i, warning in enumerate(results["warned"]):
module.warned.append(
("module_todo", warning, results["file_paths"][i]))