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20 hours ago •
nf-core
nf-core
nf-core lint fails when there are no external modules
Description of the bug
I'm trying to run nf-core linting in one of our nf-core template Nextflow pipeline that doesn't use any remote modules. Running nf-core lint throws an error - No modules from https://github.com/nf-core/modules.git installed in pipeline.
Code reference: https://github.com/nf-core/tools/blob/776089ac0e42f1fce9084182eba3b4ca0ed405e9/nf_core/components/lint/init.py#L130
This issue was raised previously in #2002 . The solution then was to use the "dev" version at that time (latest release then v2.6). To verify if the check was removed in the subsequent version, I checked version 2.7. However, it appears that version 2.7 also includes this check, as referenced below.
https://github.com/nf-core/tools/blob/5c4477b28581f8aa06dc0a49eec2c63dc88adfdd/nf_core/modules/lint/init.py#L105
Command used and terminal output
$ nf-core lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.12.1 - https://nf-co.re
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/santhanagopalan/Repos/cart/cart-env/bin/nf-core:8 in <module> │
│ │
│ 5 from nf_core.__main__ import run_nf_core │
│ 6 if __name__ == '__main__': │
│ 7 │ sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0]) │
│ ❱ 8 │ sys.exit(run_nf_core()) │
│ 9 │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/nf_core/__main__.py:141 │
│ in run_nf_core │
│ │
│ 138 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 139 │ │ stderr.print("\n") │
│ 140 │ # Launch the click cli │
│ ❱ 141 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 142 │
│ 143 │
│ 144 @tui() │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/click/core.py:1157 in │
│ __call__ │
│ │
│ 1154 │ │
│ 1155 │ def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 1156 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1157 │ │ return self.main(*args, **kwargs) │
│ 1158 │
│ 1159 │
│ 1160 class Command(BaseCommand): │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/rich_click/rich_command. │
│ py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(ctx) │
│ 127 │ │ │ │ │ if not standalone_mode: │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/click/core.py:1688 in │
│ invoke │
│ │
│ 1685 │ │ │ │ super().invoke(ctx) │
│ 1686 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1687 │ │ │ │ with sub_ctx: │
│ ❱ 1688 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1689 │ │ │
│ 1690 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1691 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/click/core.py:1434 in │
│ invoke │
│ │
│ 1431 │ │ │ echo(style(message, fg="red"), err=True) │
│ 1432 │ │ │
│ 1433 │ │ if self.callback is not None: │
│ ❱ 1434 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1435 │ │
│ 1436 │ def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]: │
│ 1437 │ │ """Return a list of completions for the incomplete value. Looks │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/click/core.py:783 in │
│ invoke │
│ │
│ 780 │ │ │
│ 781 │ │ with augment_usage_errors(__self): │
│ 782 │ │ │ with ctx: │
│ ❱ 783 │ │ │ │ return __callback(*args, **kwargs) │
│ 784 │ │
│ 785 │ def forward( │
│ 786 │ │ __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any # noqa: B902 │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/click/decorators.py:33 │
│ in new_func │
│ │
│ 30 │ """ │
│ 31 │ │
│ 32 │ def new_func(*args: "P.args", **kwargs: "P.kwargs") -> "R": │
│ ❱ 33 │ │ return f(get_current_context(), *args, **kwargs) │
│ 34 │ │
│ 35 │ return update_wrapper(new_func, f) │
│ 36 │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/nf_core/__main__.py:607 │
│ in lint │
│ │
│ 604 │ │
│ 605 │ # Run the lint tests! │
│ 606 │ try: │
│ ❱ 607 │ │ lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( │
│ 608 │ │ │ dir, │
│ 609 │ │ │ release, │
│ 610 │ │ │ fix, │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/nf_core/lint/__init__.py │
│ :94 in run_linting │
│ │
│ 91 │ lint_obj._list_files() │
│ 92 │ │
│ 93 │ # Create the modules lint object │
│ ❱ 94 │ module_lint_obj = nf_core.modules.lint.ModuleLint(pipeline_dir, hide_progress=hide_p │
│ 95 │ # Create the subworkflows lint object │
│ 96 │ try: │
│ 97 │ │ subworkflow_lint_obj = nf_core.subworkflows.lint.SubworkflowLint(pipeline_dir, h │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/nf_core/modules/lint/__i │
│ nit__.py:51 in __init__ │
│ │
│ 48 │ │ registry=None, │
│ 49 │ │ hide_progress=False, │
│ 50 │ ): │
│ ❱ 51 │ │ super().__init__( │
│ 52 │ │ │ component_type="modules", │
│ 53 │ │ │ dir=dir, │
│ 54 │ │ │ fail_warned=fail_warned, │
│ │
│ /Users/santhanagopalan/Repos/cart/cart-env/lib/python3.11/site-packages/nf_core/components/lint/ │
│ __init__.py:100 in __init__ │
│ │
│ 97 │ │ │ │ │ │ ) │
│ 98 │ │ │ │ │ ) │
│ 99 │ │ │ if not self.all_remote_components: │
│ ❱ 100 │ │ │ │ raise LookupError( │
│ 101 │ │ │ │ │ f"No {self.component_type} from {self.modules_repo.remote_url} insta │
│ 102 │ │ │ │ ) │
│ 103 │ │ │ local_component_dir = Path(self.dir, self.component_type, "local") │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
LookupError: No modules from https://github.com/nf-core/modules.git installed in pipeline.
System information
Nextflow version: 23.10.0 Hardware: MacOS M1 Executor: Local OS: macOS Monterey nf-core/tools version: v2.12.1 Python version: 3.11
