nf-core pipelines launch ends in a stacktrace

[mahesh-panchal]

Description of the bug

I'm trying to write out the params file for various pipelines in my directory, but it results in a stack trace when using the command-line option for fetchngs.

nf-core pipelines launch fetchngs


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.2.0 - https://nf-co.re


INFO     NOTE: This tool ignores any pipeline parameter defaults overwritten by Nextflow config files or   
         profiles                                                                                          
                                                                                                           
WARNING  Could not find GitHub authentication token. Some API requests may fail.                           
? Select release / branch: 1.12.0  [release]
INFO     Downloading workflow: nf-core/fetchngs (1.12.0)                                                   
ERROR    [✗] Pipeline schema does not follow nf-core specs:                                                
          Schema is using the wrong draft: http://json-schema.org/draft-07/schema, should be               
         https://json-schema.org/draft-07/schema                                                           
INFO     No pipeline schema found - creating one from the config                                           
INFO     Would you like to enter pipeline parameters using a web-based interface or a command-line wizard? 
? Choose launch method Command line
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.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-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/nf_core/__main__.py:182 in run_nf_core                                                │
│                                                                                                  │
│    179 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    180 │   │   stderr.print("\n")                                                                │
│    181 │   # Launch the click cli                                                                │
│ ❱  182 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    183                                                                                           │
│    184                                                                                           │
│    185 @tui(                                                                                     │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/rich_click/rich_command.py:378 in __call__                                            │
│                                                                                                  │
│   375 │   │   # Include this here because I run into a false warning                             │
│   376 │   │   # in the PyCharm IDE otherwise; for some reason PyCharm doesn't                    │
│   377 │   │   # seem to think RichGroups are callable. (No issues with Mypy, though.)            │
│ ❱ 378 │   │   return super().__call__(*args, **kwargs)                                           │
│   379                                                                                            │
│   380                                                                                            │
│   381 class RichCommandCollection(CommandCollection, RichGroup):                                 │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/click/core.py:1161 in __call__                                                        │
│                                                                                                  │
│   1158 │                                                                                         │
│   1159 │   def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any:                           │
│   1160 │   │   """Alias for :meth:`main`."""                                                     │
│ ❱ 1161 │   │   return self.main(*args, **kwargs)                                                 │
│   1162                                                                                           │
│   1163                                                                                           │
│   1164 class Command(BaseCommand):                                                               │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/rich_click/rich_command.py:166 in main                                                │
│                                                                                                  │
│   163 │   │   try:                                                                               │
│   164 │   │   │   try:                                                                           │
│   165 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                   │
│ ❱ 166 │   │   │   │   │   rv = self.invoke(ctx)                                                  │
│   167 │   │   │   │   │   if not standalone_mode:                                                │
│   168 │   │   │   │   │   │   return rv                                                          │
│   169 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!                                │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/click/core.py:1697 in invoke                                                          │
│                                                                                                  │
│   1694 │   │   │   │   super().invoke(ctx)                                                       │
│   1695 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1696 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1697 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1698 │   │                                                                                     │
│   1699 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1700 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/click/core.py:1697 in invoke                                                          │
│                                                                                                  │
│   1694 │   │   │   │   super().invoke(ctx)                                                       │
│   1695 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1696 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1697 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1698 │   │                                                                                     │
│   1699 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1700 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/click/core.py:1443 in invoke                                                          │
│                                                                                                  │
│   1440 │   │   │   echo(style(message, fg="red"), err=True)                                      │
│   1441 │   │                                                                                     │
│   1442 │   │   if self.callback is not None:                                                     │
│ ❱ 1443 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │
│   1444 │                                                                                         │
│   1445 │   def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]:  │
│   1446 │   │   """Return a list of completions for the incomplete value. Looks                   │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/click/core.py:788 in invoke                                                           │
│                                                                                                  │
│    785 │   │                                                                                     │
│    786 │   │   with augment_usage_errors(__self):                                                │
│    787 │   │   │   with ctx:                                                                     │
│ ❱  788 │   │   │   │   return __callback(*args, **kwargs)                                        │
│    789 │                                                                                         │
│    790 │   def forward(__self, __cmd: "Command", *args: t.Any, **kwargs: t.Any) -> t.Any:        │
│    791 │   │   """Similar to :meth:`invoke` but fills in default keyword                         │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-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/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/nf_core/__main__.py:551 in command_pipelines_launch                                   │
│                                                                                                  │
│    548 │   """                                                                                   │
│    549 │   Launch a pipeline using a web GUI or command line prompts.                            │
│    550 │   """                                                                                   │
│ ❱  551 │   pipelines_launch(ctx, pipeline, id, revision, command_only, params_in, params_out, s  │
│    552                                                                                           │
│    553                                                                                           │
│    554 # nf-core pipelines list                                                                  │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/nf_core/commands_pipelines.py:264 in pipelines_launch                                 │
│                                                                                                  │
│   261 │   │   url,                                                                               │
│   262 │   │   id,                                                                                │
│   263 │   )                                                                                      │
│ ❱ 264 │   if not launcher.launch_pipeline():                                                     │
│   265 │   │   sys.exit(1)                                                                        │
│   266                                                                                            │
│   267                                                                                            │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/nf_core/pipelines/launch.py:176 in launch_pipeline                                    │
│                                                                                                  │
│   173 │   │   │   │   │   return False                                                           │
│   174 │   │   │   else:                                                                          │
│   175 │   │   │   │   # Kick off the interactive wizard to collect user inputs                   │
│ ❱ 176 │   │   │   │   self.prompt_schema()                                                       │
│   177 │   │                                                                                      │
│   178 │   │   # Validate the parameters that we now have                                         │
│   179 │   │   if not self.schema_obj.validate_params():                                          │
│                                                                                                  │
│ /Users/mahpa906/Documents/Projects/nf-metaomics-daisychain/.pixi/envs/default/lib/python3.13/sit │
│ e-packages/nf_core/pipelines/launch.py:412 in prompt_schema                                      │
│                                                                                                  │
│   409 │   │   definitions_schemas = self.schema_obj.schema.get("$defs", self.schema_obj.schema   │
│   410 │   │   for allOf in self.schema_obj.schema.get("allOf", []):                              │
│   411 │   │   │   d_key = allOf["$ref"][14:]                                                     │
│ ❱ 412 │   │   │   answers.update(self.prompt_group(d_key, definitions_schemas[d_key]))           │
│   413 │   │                                                                                      │
│   414 │   │   # Top level schema params                                                          │
│   415 │   │   for param_id, param_obj in self.schema_obj.schema.get("properties", {}).items():   │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: 'dict_items' object is not subscriptable

Command used and terminal output

System information

No response