$ nf-core modules info samtools/view
<frozen importlib._bootstrap>:491: RuntimeWarning: The global interpreter lock (GIL) has been enabled to load module '_brotli', which has not declared that it can run safely without the GIL. To override this behavior and keep the GIL disabled (at your own risk), run with PYTHON_GIL=0 or -Xgil=0.
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|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 4.0.2 - https://nf-co.re
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/bin/nf-core:10 in <module> │
│ │
│ 7 │
│ 8 if __name__ == '__main__': │
│ 9 │ sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) │
│ ❱ 10 │ sys.exit(run_nf_core()) │
│ 11 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/nf_core/__main__.py:130 in run_nf_core │
│ │
│ 127 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 128 │ │ stderr.print("\n") │
│ 129 │ # Launch the click cli │
│ ❱ 130 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 131 │
│ 132 │
│ 133 @tui(command="interface", help="Launch the nf-core interface") │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/rich_click/rich_command.py:402 in __call__ │
│ │
│ 399 │ │ # Include this here because I run into a false warning │
│ 400 │ │ # in the PyCharm IDE otherwise; for some reason PyCharm doesn't │
│ 401 │ │ # seem to think RichGroups are callable. (No issues with Mypy, though.) │
│ ❱ 402 │ │ return super().__call__(*args, **kwargs) │
│ 403 │ │
│ 404 │ @overload │
│ 405 │ def command(self, __func: Callable[..., Any]) -> RichCommand: ... │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/core.py:1514 in __call__ │
│ │
│ 1511 │ │
│ 1512 │ def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 1513 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1514 │ │ return self.main(*args, **kwargs) │
│ 1515 │
│ 1516 │
│ 1517 class _FakeSubclassCheck(type): │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/rich_click/rich_command.py:216 in main │
│ │
│ 213 │ │ try: │
│ 214 │ │ │ try: │
│ 215 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 216 │ │ │ │ │ rv = self.invoke(ctx) │
│ 217 │ │ │ │ │ if not standalone_mode: │
│ 218 │ │ │ │ │ │ return rv │
│ 219 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/core.py:1902 in invoke │
│ │
│ 1899 │ │ │ │ super().invoke(ctx) │
│ 1900 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1901 │ │ │ │ with sub_ctx: │
│ ❱ 1902 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1903 │ │ │
│ 1904 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1905 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/core.py:1902 in invoke │
│ │
│ 1899 │ │ │ │ super().invoke(ctx) │
│ 1900 │ │ │ │ sub_ctx = cmd.make_context(cmd_name, args, parent=ctx) │
│ 1901 │ │ │ │ with sub_ctx: │
│ ❱ 1902 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1903 │ │ │
│ 1904 │ │ # In chain mode we create the contexts step by step, but after the │
│ 1905 │ │ # base command has been invoked. Because at that point we do not │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/core.py:1298 in invoke │
│ │
│ 1295 │ │ │ echo(style(message, fg="red"), err=True) │
│ 1296 │ │ │
│ 1297 │ │ if self.callback is not None: │
│ ❱ 1298 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1299 │ │
│ 1300 │ def shell_complete(self, ctx: Context, incomplete: str) -> list[CompletionItem]: │
│ 1301 │ │ """Return a list of completions for the incomplete value. Looks │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/core.py:853 in invoke │
│ │
│ 850 │ │ │
│ 851 │ │ with augment_usage_errors(self): │
│ 852 │ │ │ with ctx: │
│ ❱ 853 │ │ │ │ return callback(*args, **kwargs) │
│ 854 │ │
│ 855 │ def forward(self, cmd: Command, /, *args: t.Any, **kwargs: t.Any) -> t.Any: │
│ 856 │ │ """Similar to :meth:`invoke` but fills in default keyword │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/click/decorators.py:34 in new_func │
│ │
│ 31 │ """ │
│ 32 │ │
│ 33 │ def new_func(*args: P.args, **kwargs: P.kwargs) -> R: │
│ ❱ 34 │ │ return f(get_current_context(), *args, **kwargs) │
│ 35 │ │
│ 36 │ return update_wrapper(new_func, f) │
│ 37 │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/nf_core/__main__.py:1399 in command_modules_info │
│ │
│ 1396 │ """ │
│ 1397 │ Show developer usage information about a given module. │
│ 1398 │ """ │
│ ❱ 1399 │ modules_info(ctx, tool, directory) │
│ 1400 │
│ 1401 │
│ 1402 # nf-core modules bump-versions │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/nf_core/commands_modules.py:307 in modules_info │
│ │
│ 304 │ │ │ ctx.obj["modules_repo_branch"], │
│ 305 │ │ │ ctx.obj["modules_repo_no_pull"], │
│ 306 │ │ ) │
│ ❱ 307 │ │ stdout.print(module_info.get_component_info()) │
│ 308 │ except (UserWarning, LookupError) as e: │
│ 309 │ │ log.error(e) │
│ 310 │ │ sys.exit(1) │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/nf_core/components/info.py:173 in get_component_info │
│ │
│ 170 │ │ if self.meta is None: │
│ 171 │ │ │ raise UserWarning(f"Could not find {self.component_type[:-1]} '{self.compone │
│ 172 │ │ │
│ ❱ 173 │ │ return self.generate_component_info_help() │
│ 174 │ │
│ 175 │ def get_local_yaml(self) -> dict | None: │
│ 176 │ │ """Attempt to get the meta.yml file from a locally installed module/subworkflow. │
│ │
│ /Users/mahpa906/Documents/Projects/nf-core-aMeta/.pixi/envs/default/lib/python3.14t/site-package │
│ s/nf_core/components/info.py:306 in generate_component_info_help │
│ │
│ 303 │ │ │ │ inputs_table.add_row(f"[italic]input[{i}][/]", "", "") │
│ 304 │ │ │ │ if self.component_type == "modules": │
│ 305 │ │ │ │ │ for element in input_channel: │
│ ❱ 306 │ │ │ │ │ │ for key, info in element.items(): │
│ 307 │ │ │ │ │ │ │ inputs_table.add_row( │
│ 308 │ │ │ │ │ │ │ │ f"[orange1 on black] {key} [/][dim i] ({info['type']})", │
│ 309 │ │ │ │ │ │ │ │ Markdown(info["description"] if info["description"] else │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
AttributeError: 'str' object has no attribute 'items'
Description of the bug
nf-core modules info samtools/viewresults in a stack trace.Command used and terminal output
System information
No response