Linting throws an error if hyphens appear in the name

[adamrtalbot]

Description of the bug

When linting a pipeline with a hyphen in the name nf-core pipelines lint throws an error. It shouldn't do this because I can call my pipeline whatever the heck I want.

Command used and terminal output

adamtalbot@vm-adamtalbot:~/wgs-pipeline$ nf-core pipelines lint


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

    nf-core/tools version 2.14.2.dev0 - https://nf-co.re


INFO     Testing pipeline: .                                                                                                                                                                                                                                                                                                                                                                                  
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/adamtalbot/.local/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/adamtalbot/.local/lib/python3.10/site-packages/nf_core/__main__.py:180 in run_nf_core      │
│                                                                                                  │
│    177 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    178 │   │   stderr.print("\n")                                                                │
│    179 │   # Launch the click cli                                                                │
│ ❱  180 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    181                                                                                           │
│    182                                                                                           │
│    183 @tui(                                                                                     │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/rich_click/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):                                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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):                                                               │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/rich_click/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!                                │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                   │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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             │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                                                                                            │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/__main__.py:348 in                  │
│ command_pipelines_lint                                                                           │
│                                                                                                  │
│    345 │   """                                                                                   │
│    346 │   Check pipeline code against nf-core guidelines.                                       │
│    347 │   """                                                                                   │
│ ❱  348 │   pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned,   │
│    349                                                                                           │
│    350                                                                                           │
│    351 # nf-core pipelines download                                                              │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/commands_pipelines.py:133 in        │
│ pipelines_lint                                                                                   │
│                                                                                                  │
│   130 │                                                                                          │
│   131 │   # Run the lint tests!                                                                  │
│   132 │   try:                                                                                   │
│ ❱ 133 │   │   lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(                     │
│   134 │   │   │   dir,                                                                           │
│   135 │   │   │   release,                                                                       │
│   136 │   │   │   fix,                                                                           │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:603 in   │
│ run_linting                                                                                      │
│                                                                                                  │
│   600 │                                                                                          │
│   601 │   # Run the pipeline linting tests                                                       │
│   602 │   try:                                                                                   │
│ ❱ 603 │   │   lint_obj._lint_pipeline()                                                          │
│   604 │   except AssertionError as e:                                                            │
│   605 │   │   log.critical(f"Critical error: {e}")                                               │
│   606 │   │   log.info("Stopping tests...")                                                      │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:228 in   │
│ _lint_pipeline                                                                                   │
│                                                                                                  │
│   225 │   │   │   │   │   continue                                                               │
│   226 │   │   │   │   self.progress_bar.update(lint_progress, advance=1, test_name=test_name)    │
│   227 │   │   │   │   log.debug(f"Running lint test: {test_name}")                               │
│ ❱ 228 │   │   │   │   test_results = getattr(self, test_name)()                                  │
│   229 │   │   │   │   for test in test_results.get("passed", []):                                │
│   230 │   │   │   │   │   self.passed.append((test_name, test))                                  │
│   231 │   │   │   │   for test in test_results.get("ignored", []):                               │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/files_unchanged.py:1 │
│ 30 in files_unchanged                                                                            │
│                                                                                                  │
│   127 │   │   yaml.dump(template_yaml, fh, default_flow_style=False)                             │
│   128 │                                                                                          │
│   129 │   test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")                    │
│ ❱ 130 │   create_obj = nf_core.pipelines.create.create.PipelineCreate(                           │
│   131 │   │   None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=templat   │
│   132 │   )                                                                                      │
│   133 │   create_obj.init_pipeline()                                                             │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:74 in    │
│ __init__                                                                                         │
│                                                                                                  │
│    71 │   │   │   template_config and (isinstance(template_config, str) or isinstance(template   │
│    72 │   │   ):                                                                                 │
│    73 │   │   │   # Obtain a CreateConfig object from the template yaml file                     │
│ ❱  74 │   │   │   self.config = self.check_template_yaml_info(template_config, name, descripti   │
│    75 │   │   │   self.update_config(organisation, version, force, outdir)                       │
│    76 │   │   else:                                                                              │
│    77 │   │   │   raise UserWarning("The template configuration was not provided.")              │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:138 in   │
│ check_template_yaml_info                                                                         │
│                                                                                                  │
│   135 │   │   │   try:                                                                           │
│   136 │   │   │   │   with open(template_yaml) as f:                                             │
│   137 │   │   │   │   │   template_yaml = yaml.safe_load(f)                                      │
│ ❱ 138 │   │   │   │   │   config = CreateConfig(**template_yaml)                                 │
│   139 │   │   │   except FileNotFoundError:                                                      │
│   140 │   │   │   │   raise UserWarning(f"Template YAML file '{template_yaml}' not found.")      │
│   141                                                                                            │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/utils.py:53 in     │
│ __init__                                                                                         │
│                                                                                                  │
│    50 │                                                                                          │
│    51 │   def __init__(self, /, **data: Any) -> None:                                            │
│    52 │   │   """Custom init method to allow using a context on the model initialization."""     │
│ ❱  53 │   │   self.__pydantic_validator__.validate_python(                                       │
│    54 │   │   │   data,                                                                          │
│    55 │   │   │   self_instance=self,                                                            │
│    56 │   │   │   context=_init_context_var.get(),                                               │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ValidationError: 1 validation error for CreateConfig
name
  Value error, Must not contain special characters. Only '-' or '_' are allowed. [type=value_error, input_value='wgs-pipeline', input_type=str]

### System information

Using dev build on commit 930ece572bf23b68c7a7c5259e918a878ba6499e

[mashehu]

what pipeline name did you try?

[mirpedrol]

Hi @adamrtalbot, hyphens are allowed in custom pipelines, how did you create your pipeline? I tested this behaviour and lining passes for me.
I opened #3094 to also allow numbers, for instance myorg-this-isap1pe_ did work when I tested that PR.

[adamrtalbot]

what pipeline name did you try?

wgs-pipeline

Still seeing the error with 930ece5

adamtalbot@vm-adamtalbot:~/wgs-pipeline$ nf-core --verbose pipelines lint


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

    nf-core/tools version 2.14.2.dev0 - https://nf-co.re


DEBUG    Popen(['git', 'cat-file', '--batch-check'], cwd=/home/adamtalbot/wgs-pipeline, stdin=<valid stream>, shell=False, universal_newlines=False)                                                                                                                                                                            cmd.py:1253
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                                                                                                          utils.py:1060
DEBUG    Got '.' as path                                                                                                                                                                                                                                                                                                           utils.py:244
DEBUG    Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json                                                                                                                                                                                                          utils.py:278
DEBUG    Popen(['git', 'version'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                                                          cmd.py:1253
DEBUG    Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                        cmd.py:1253
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                                               cmd.py:1253
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                                           cmd.py:1253
DEBUG    Using config file: /home/adamtalbot/.config/nfcore/nf-core/modules/.nf-core.yml                                                                                                                                                                                                                                          utils.py:1060
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                                                                                                          utils.py:1060
DEBUG    The following files were modified by prettier:                                                                                                                                                                                                                                                                        lint_utils.py:88
                                                                                                                                                                                                                                                                                                                                               
         modules.json                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                               
DEBUG    Got '.' as path                                                                                                                                                                                                                                                                                                           utils.py:244
DEBUG    Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json                                                                                                                                                                                                          utils.py:278
DEBUG    Registry set to quay.io                                                                                                                                                                                                                                                                                                __init__.py:141
DEBUG    Popen(['git', 'checkout', 'master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                                               cmd.py:1253
DEBUG    Popen(['git', 'merge', 'origin/master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)                                                                                                                                                                           cmd.py:1253
DEBUG    Using config file: /home/adamtalbot/.config/nfcore/nf-core/modules/.nf-core.yml                                                                                                                                                                                                                                          utils.py:1060
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                                                                                                          utils.py:1060
DEBUG    The following files were modified by prettier:                                                                                                                                                                                                                                                                        lint_utils.py:88
                                                                                                                                                                                                                                                                                                                                               
         modules.json                                                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                               
DEBUG    Got '.' as path                                                                                                                                                                                                                                                                                                           utils.py:244
DEBUG    Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json                                                                                                                                                                                                          utils.py:278
DEBUG    Registry set to quay.io                                                                                                                                                                                                                                                                                                __init__.py:141
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                                                                                                          utils.py:1060
DEBUG    Using config file: .nf-core.yml                                                                                                                                                                                                                                                                                          utils.py:1060
INFO     Testing pipeline: .                                                                                                                                                                                                                                                                                                    __init__.py:164
DEBUG    Running lint test: files_exist                                                                                                                                                                                                                                                                                         __init__.py:227
DEBUG    Found plugins in nextflow.config with value nf-validation                                                                                                                                                                                                                                                           files_exist.py:252
DEBUG    Running lint test: nextflow_config                                                                                                                                                                                                                                                                                     __init__.py:227
DEBUG    JSON file loaded: nextflow_schema.json                                                                                                                                                                                                                                                                                   schema.py:119
DEBUG    Running lint test: files_unchanged                                                                                                                                                                                                                                                                                     __init__.py:227
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/adamtalbot/.local/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/adamtalbot/.local/lib/python3.10/site-packages/nf_core/__main__.py:180 in run_nf_core      │
│                                                                                                  │
│    177 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    178 │   │   stderr.print("\n")                                                                │
│    179 │   # Launch the click cli                                                                │
│ ❱  180 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    181                                                                                           │
│    182                                                                                           │
│    183 @tui(                                                                                     │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/rich_click/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):                                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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):                                                               │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/rich_click/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!                                │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                 │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                   │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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             │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/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                                                                                            │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/__main__.py:348 in                  │
│ command_pipelines_lint                                                                           │
│                                                                                                  │
│    345 │   """                                                                                   │
│    346 │   Check pipeline code against nf-core guidelines.                                       │
│    347 │   """                                                                                   │
│ ❱  348 │   pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned,   │
│    349                                                                                           │
│    350                                                                                           │
│    351 # nf-core pipelines download                                                              │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/commands_pipelines.py:133 in        │
│ pipelines_lint                                                                                   │
│                                                                                                  │
│   130 │                                                                                          │
│   131 │   # Run the lint tests!                                                                  │
│   132 │   try:                                                                                   │
│ ❱ 133 │   │   lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting(                     │
│   134 │   │   │   dir,                                                                           │
│   135 │   │   │   release,                                                                       │
│   136 │   │   │   fix,                                                                           │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:603 in   │
│ run_linting                                                                                      │
│                                                                                                  │
│   600 │                                                                                          │
│   601 │   # Run the pipeline linting tests                                                       │
│   602 │   try:                                                                                   │
│ ❱ 603 │   │   lint_obj._lint_pipeline()                                                          │
│   604 │   except AssertionError as e:                                                            │
│   605 │   │   log.critical(f"Critical error: {e}")                                               │
│   606 │   │   log.info("Stopping tests...")                                                      │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:228 in   │
│ _lint_pipeline                                                                                   │
│                                                                                                  │
│   225 │   │   │   │   │   continue                                                               │
│   226 │   │   │   │   self.progress_bar.update(lint_progress, advance=1, test_name=test_name)    │
│   227 │   │   │   │   log.debug(f"Running lint test: {test_name}")                               │
│ ❱ 228 │   │   │   │   test_results = getattr(self, test_name)()                                  │
│   229 │   │   │   │   for test in test_results.get("passed", []):                                │
│   230 │   │   │   │   │   self.passed.append((test_name, test))                                  │
│   231 │   │   │   │   for test in test_results.get("ignored", []):                               │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/files_unchanged.py:1 │
│ 30 in files_unchanged                                                                            │
│                                                                                                  │
│   127 │   │   yaml.dump(template_yaml, fh, default_flow_style=False)                             │
│   128 │                                                                                          │
│   129 │   test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}")                    │
│ ❱ 130 │   create_obj = nf_core.pipelines.create.create.PipelineCreate(                           │
│   131 │   │   None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=templat   │
│   132 │   )                                                                                      │
│   133 │   create_obj.init_pipeline()                                                             │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:74 in    │
│ __init__                                                                                         │
│                                                                                                  │
│    71 │   │   │   template_config and (isinstance(template_config, str) or isinstance(template   │
│    72 │   │   ):                                                                                 │
│    73 │   │   │   # Obtain a CreateConfig object from the template yaml file                     │
│ ❱  74 │   │   │   self.config = self.check_template_yaml_info(template_config, name, descripti   │
│    75 │   │   │   self.update_config(organisation, version, force, outdir)                       │
│    76 │   │   else:                                                                              │
│    77 │   │   │   raise UserWarning("The template configuration was not provided.")              │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:145 in   │
│ check_template_yaml_info                                                                         │
│                                                                                                  │
│   142 │   │   │   try:                                                                           │
│   143 │   │   │   │   with open(template_yaml) as f:                                             │
│   144 │   │   │   │   │   template_yaml = yaml.safe_load(f)                                      │
│ ❱ 145 │   │   │   │   │   config = CreateConfig(**template_yaml)                                 │
│   146 │   │   │   except FileNotFoundError:                                                      │
│   147 │   │   │   │   raise UserWarning(f"Template YAML file '{template_yaml}' not found.")      │
│   148                                                                                            │
│                                                                                                  │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/utils.py:53 in     │
│ __init__                                                                                         │
│                                                                                                  │
│    50 │                                                                                          │
│    51 │   def __init__(self, /, **data: Any) -> None:                                            │
│    52 │   │   """Custom init method to allow using a context on the model initialization."""     │
│ ❱  53 │   │   self.__pydantic_validator__.validate_python(                                       │
│    54 │   │   │   data,                                                                          │
│    55 │   │   │   self_instance=self,                                                            │
│    56 │   │   │   context=_init_context_var.get(),                                               │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ValidationError: 1 validation error for CreateConfig
name
  Value error, Must not contain special characters. Only '-' or '_' are allowed. [type=value_error, input_value='wgs-pipeline', input_type=str]
    For further information visit https://errors.pydantic.dev/2.8/v/value_error

[adamrtalbot]

Hmm might not be hyphens, let me try something.

[adamrtalbot]

Blegh, my bad. Solved it.