AttributeError with nf-core pipelines create-params-file

[matbonfanti]

Description of the bug

When running the command nf-core pipelines create-params-file, and AttributeError exception is raised because inside the function write_params_file() (method of ParamsFileBuilder) the first argument is assumed to be a Path object, instead it is passed a variable that is a string with the name of the output parameter file.

Command used and terminal output

$ nf-core pipelines create-params-file -x --force --output ./nf-params.yml  nf-core/sarek

---


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

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


INFO     Downloading workflow: nf-core/sarek (None)
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/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                                                                                              │
│                                                                                                  │
│ /home/matteo/source/nfcore-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(                                                                                     │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-packages/rich_click/rich_comma │
│ nd.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):                                 │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-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):                                                               │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-packages/rich_click/rich_comma │
│ nd.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!                                │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-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                 │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-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                 │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-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                   │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-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                         │
│                                                                                                  │
│ /home/matteo/miniconda3/envs/nfcore-tools-dev/lib/python3.12/site-packages/click/decorators.py:3 │
│ 3 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                                                                                            │
│                                                                                                  │
│ /home/matteo/source/nfcore-tools/nf_core/__main__.py:486 in command_pipelines_create_params_file │
│                                                                                                  │
│    483 │   """                                                                                   │
│    484 │   Build a parameter file for a pipeline.                                                │
│    485 │   """                                                                                   │
│ ❱  486 │   pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hidden)     │
│    487                                                                                           │
│    488                                                                                           │
│    489 # nf-core pipelines launch                                                                │
│                                                                                                  │
│ /home/matteo/source/nfcore-tools/nf_core/commands_pipelines.py:221 in                            │
│ pipelines_create_params_file                                                                     │
│                                                                                                  │
│   218 │   """                                                                                    │
│   219 │   builder = ParamsFileBuilder(pipeline, revision)                                        │
│   220 │                                                                                          │
│ ❱ 221 │   if not builder.write_params_file(output, show_hidden=show_hidden, force=force):        │
│   222 │   │   sys.exit(1)                                                                        │
│   223                                                                                            │
│   224                                                                                            │
│                                                                                                  │
│ /home/matteo/source/nfcore-tools/nf_core/pipelines/params_file.py:282 in write_params_file       │
│                                                                                                  │
│   279 │   │                                                                                      │
│   280 │   │   schema_out = self.generate_params_file(show_hidden=show_hidden)                    │
│   281 │   │                                                                                      │
│ ❱ 282 │   │   if output_fn.exists() and not force:                                               │
│   283 │   │   │   log.error(f"File '{output_fn}' exists! Please delete first, or use '--force'   │
│   284 │   │   │   return False                                                                   │
│   285 │   │   output_fn.write_text(schema_out)                                                   │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
AttributeError: 'str' object has no attribute 'exists'

System information

• nextflow 24.10.4
• laptop
• local executor
• linux WSL2 (Ubuntu 20.04.6 LTS) on Windows
• nf-core/tools version 3.2.0 and development version f332e85 (tried both)
• python 3.12.8 and 3.9.15 (tried both)

[matbonfanti]

Bug has been fixed by PR #3435, create-params-file works with the current devel version.