Testing does not work for subworkflows

[nikhil]

Description of the bug

When migrating tests from pytests to nf-test, I hit a unhandled traceback.

Command used and terminal output

nf-core subworkflows test subworkflows/bam_qc_picard

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

    nf-core/tools version 2.11.dev0 - https://nf-co.re

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /opt/conda/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                                                                                              │
│                                                                                                  │
│ /opt/conda/lib/python3.11/site-packages/nf_core/__main__.py:111 in run_nf_core                   │
│                                                                                                  │
│    108 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    109 │   │   stderr.print("\n")                                                                │
│    110 │   # Launch the click cli                                                                │
│ ❱  111 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    112                                                                                           │
│    113                                                                                           │
│    114 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))                   │
│                                                                                                  │
│ /opt/conda/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):                                                               │
│                                                                                                  │
│ /opt/conda/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!                                │
│                                                                                                  │
│ /opt/conda/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                 │
│                                                                                                  │
│ /opt/conda/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                 │
│                                                                                                  │
│ /opt/conda/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                   │
│                                                                                                  │
│ /opt/conda/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             │
│                                                                                                  │
│ /opt/conda/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                                                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
TypeError: test_subworkflow() got an unexpected keyword argument 'run_tests'

System information

Nextflow version: 23.04.3 Hardware: Cloud/gitpod Executor: local OS: Linux verion of nf-core/tools: 2.11.dev0 Python version: 3.11.5

[mashehu]

fixed with #2546