modules lint can't handle nested environment.yml files

[mashehu]

Description of the bug

As shown in nf-core/modules#7399 nf-core tools breaks for correctly formated environment yaml files, that contain pip dependencies, e.g. https://github.com/nf-core/modules/blob/efd030110f637f845fbefc1120c2724bd852aa41/modules/nf-core/doubletdetection/environment.yml

Command used and terminal output

nf-core modules lint doubletdetection


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

    nf-core/tools version 3.3.0.dev0 - https://nf-co.re


INFO     Linting modules repo: '.'
INFO     Linting module: 'doubletdetection'
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/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/mitochondrium/tools/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(                                                                                     │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/site-packages/rich_c │
│ lick/rich_command.py:367 in __call__                                                             │
│                                                                                                  │
│   364 │   │   # Include this here because I run into a false warning                             │
│   365 │   │   # in the PyCharm IDE otherwise; for some reason PyCharm doesn't                    │
│   366 │   │   # seem to think RichGroups are callable. (No issues with Mypy, though.)            │
│ ❱ 367 │   │   return super().__call__(*args, **kwargs)                                           │
│   368                                                                                            │
│   369                                                                                            │
│   370 class RichCommandCollection(CommandCollection, RichGroup):                                 │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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):                                                               │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/site-packages/rich_c │
│ lick/rich_command.py:152 in main                                                                 │
│                                                                                                  │
│   149 │   │   try:                                                                               │
│   150 │   │   │   try:                                                                           │
│   151 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                   │
│ ❱ 152 │   │   │   │   │   rv = self.invoke(ctx)                                                  │
│   153 │   │   │   │   │   if not standalone_mode:                                                │
│   154 │   │   │   │   │   │   return rv                                                          │
│   155 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!                                │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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                 │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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                 │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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                   │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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             │
│                                                                                                  │
│ /opt/homebrew/Caskroom/miniconda/base/envs/nfcore-tools-py3_8/lib/python3.8/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/mitochondrium/tools/nf_core/__main__.py:1299 in command_modules_lint                      │
│                                                                                                  │
│   1296 │   """                                                                                   │
│   1297 │   Lint one or more modules in a directory.                                              │
│   1298 │   """                                                                                   │
│ ❱ 1299 │   modules_lint(ctx, tool, directory, registry, key, all, fail_warned, local, passed, s  │
│   1300                                                                                           │
│   1301                                                                                           │
│   1302 # nf-core modules info                                                                    │
│                                                                                                  │
│ /Users/mitochondrium/tools/nf_core/commands_modules.py:288 in modules_lint                       │
│                                                                                                  │
│   285 │   │   │   no_pull=ctx.obj["modules_repo_no_pull"],                                       │
│   286 │   │   │   hide_progress=ctx.obj["hide_progress"],                                        │
│   287 │   │   )                                                                                  │
│ ❱ 288 │   │   module_lint.lint(                                                                  │
│   289 │   │   │   module=tool,                                                                   │
│   290 │   │   │   registry=registry,                                                             │
│   291 │   │   │   key=key,                                                                       │
│                                                                                                  │
│ /Users/mitochondrium/tools/nf_core/modules/lint/__init__.py:174 in lint                          │
│                                                                                                  │
│   171 │   │                                                                                      │
│   172 │   │   # Lint nf-core modules                                                             │
│   173 │   │   if not local and len(remote_modules) > 0:                                          │
│ ❱ 174 │   │   │   self.lint_modules(remote_modules, registry=registry, local=False, fix_versio   │
│   175 │   │                                                                                      │
│   176 │   │   if print_results:                                                                  │
│   177 │   │   │   self._print_results(show_passed=show_passed, sort_by=sort_by)                  │
│                                                                                                  │
│ /Users/mitochondrium/tools/nf_core/modules/lint/__init__.py:210 in lint_modules                  │
│                                                                                                  │
│   207 │   │   │                                                                                  │
│   208 │   │   │   for mod in modules:                                                            │
│   209 │   │   │   │   progress_bar.update(lint_progress, advance=1, test_name=mod.component_na   │
│ ❱ 210 │   │   │   │   self.lint_module(mod, progress_bar, local=local, fix_version=fix_version   │
│   211 │                                                                                          │
│   212 │   def lint_module(                                                                       │
│   213 │   │   self,                                                                              │
│                                                                                                  │
│ /Users/mitochondrium/tools/nf_core/modules/lint/__init__.py:278 in lint_module                   │
│                                                                                                  │
│   275 │   │   │   │   if test_name == "main_nf":                                                 │
│   276 │   │   │   │   │   getattr(self, test_name)(mod, fix_version, self.registry, progress_b   │
│   277 │   │   │   │   else:                                                                      │
│ ❱ 278 │   │   │   │   │   getattr(self, test_name)(mod)                                          │
│   279 │   │   │                                                                                  │
│   280 │   │   │   self.passed += [LintResult(mod, *m) for m in mod.passed]                       │
│   281 │   │   │   warned = [LintResult(mod, *m) for m in mod.warned]                             │
│                                                                                                  │
│ /Users/mitochondrium/tools/nf_core/modules/lint/environment_yml.py:86 in environment_yml         │
│                                                                                                  │
│    83 │   │                                                                                      │
│    84 │   │   if valid_env_yml:                                                                  │
│    85 │   │   │   # Check that the dependencies section is sorted alphabetically                 │
│ ❱  86 │   │   │   if sorted(env_yml["dependencies"]) == env_yml["dependencies"]:                 │
│    87 │   │   │   │   module.passed.append(                                                      │
│    88 │   │   │   │   │   (                                                                      │
│    89 │   │   │   │   │   │   "environment_yml_sorted",                                          │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: '<' not supported between instances of 'dict' and 'str'

System information

No response