local variable 'docker_image_name' referenced before assignment

[anoronh4]

Description of the bug

When i try to create a new module using nf-core tools i get an error. It doesn't happen when i try to create modules with other names such as bcftools/fakemodule or cell/phone. Looks like it can find a docker image but not a singularity image, and the evaluation of the following line:

tools/nf_core/utils.py

Line 734 in e5ce6ce

common_keys = list(all_docker.keys() & all_singularity.keys())

leads to a set size of 0. so a few lines down the loop is never executed because the set it's looping on is empty and docker_image_name is never instantiated and singularity_image is not updated (instantiated as None earlier in the function).

I can see that the csvtk singularity image can't be found because i run the following commands in python:

package = "csvtk"
version = "0.26.0"
biocontainers_api_url = f"https://api.biocontainers.pro/ga4gh/trs/v2/tools/{package}/versions/{package}-{version}"
response = requests.get(biocontainers_api_url)
images = response.json()["images"]
[ i['image_type'] for i in images]
# ['Conda', 'Docker']

(others show ['Conda', 'Docker', 'Singularity']

Command used and terminal output

$ nf-core modules create -d . csvtk/join

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

    nf-core/tools version 2.9 - https://nf-co.re


INFO     Repository type: modules                                                                                       
INFO     Press enter to use default values (shown in brackets) or type your own responses. ctrl+click underlined text to
         open links.                                                                                                    
INFO     Using Bioconda package: 'bioconda::csvtk=0.26.0'                                                               
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/noronhaa/anaconda3/envs/nf-core/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/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/__main__.py:110 in    │
│ run_nf_core                                                                                      │
│                                                                                                  │
│    107 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    108 │   │   stderr.print("\n")                                                                │
│    109 │   # Launch the click cli                                                                │
│ ❱  110 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    111                                                                                           │
│    112                                                                                           │
│    113 @click.group(context_settings=dict(help_option_names=["-h", "--help"]))                   │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1130 in         │
│ __call__                                                                                         │
│                                                                                                  │
│   1127 │                                                                                         │
│   1128 │   def __call__(self, *args: t.Any, **kwargs: t.Any) -> t.Any:                           │
│   1129 │   │   """Alias for :meth:`main`."""                                                     │
│ ❱ 1130 │   │   return self.main(*args, **kwargs)                                                 │
│   1131                                                                                           │
│   1132                                                                                           │
│   1133 class Command(BaseCommand):                                                               │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/rich_click/rich_group.py:21   │
│ in main                                                                                          │
│                                                                                                  │
│   18 │                                                                                           │
│   19 │   def main(self, *args, standalone_mode: bool = True, **kwargs):                          │
│   20 │   │   try:                                                                                │
│ ❱ 21 │   │   │   rv = super().main(*args, standalone_mode=False, **kwargs)                       │
│   22 │   │   │   if not standalone_mode:                                                         │
│   23 │   │   │   │   return rv                                                                   │
│   24 │   │   except click.ClickException as e:                                                   │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1055 in main    │
│                                                                                                  │
│   1052 │   │   try:                                                                              │
│   1053 │   │   │   try:                                                                          │
│   1054 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                  │
│ ❱ 1055 │   │   │   │   │   rv = self.invoke(ctx)                                                 │
│   1056 │   │   │   │   │   if not standalone_mode:                                               │
│   1057 │   │   │   │   │   │   return rv                                                         │
│   1058 │   │   │   │   │   # it's not safe to `ctx.exit(rv)` here!                               │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1657 in invoke  │
│                                                                                                  │
│   1654 │   │   │   │   super().invoke(ctx)                                                       │
│   1655 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1656 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1658 │   │                                                                                     │
│   1659 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1660 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1657 in invoke  │
│                                                                                                  │
│   1654 │   │   │   │   super().invoke(ctx)                                                       │
│   1655 │   │   │   │   sub_ctx = cmd.make_context(cmd_name, args, parent=ctx)                    │
│   1656 │   │   │   │   with sub_ctx:                                                             │
│ ❱ 1657 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))               │
│   1658 │   │                                                                                     │
│   1659 │   │   # In chain mode we create the contexts step by step, but after the                │
│   1660 │   │   # base command has been invoked.  Because at that point we do not                 │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:1404 in invoke  │
│                                                                                                  │
│   1401 │   │   │   echo(style(message, fg="red"), err=True)                                      │
│   1402 │   │                                                                                     │
│   1403 │   │   if self.callback is not None:                                                     │
│ ❱ 1404 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                │
│   1405 │                                                                                         │
│   1406 │   def shell_complete(self, ctx: Context, incomplete: str) -> t.List["CompletionItem"]:  │
│   1407 │   │   """Return a list of completions for the incomplete value. Looks                   │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/core.py:760 in invoke   │
│                                                                                                  │
│    757 │   │                                                                                     │
│    758 │   │   with augment_usage_errors(__self):                                                │
│    759 │   │   │   with ctx:                                                                     │
│ ❱  760 │   │   │   │   return __callback(*args, **kwargs)                                        │
│    761 │                                                                                         │
│    762 │   def forward(                                                                          │
│    763 │   │   __self, __cmd: "Command", *args: t.Any, **kwargs: t.Any  # noqa: B902             │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/click/decorators.py:26 in     │
│ new_func                                                                                         │
│                                                                                                  │
│    23 │   """                                                                                    │
│    24 │                                                                                          │
│    25 │   def new_func(*args, **kwargs):  # type: ignore                                         │
│ ❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                   │
│    27 │                                                                                          │
│    28 │   return update_wrapper(t.cast(F, new_func), f)                                          │
│    29                                                                                            │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/__main__.py:800 in    │
│ create_module                                                                                    │
│                                                                                                  │
│    797 │   │   module_create = ModuleCreate(                                                     │
│    798 │   │   │   dir, tool, author, label, has_meta, force, conda_name, conda_package_version  │
│    799 │   │   )                                                                                 │
│ ❱  800 │   │   module_create.create()                                                            │
│    801 │   except UserWarning as e:                                                              │
│    802 │   │   log.critical(e)                                                                   │
│    803 │   │   sys.exit(1)                                                                       │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/components/create.py: │
│ 139 in create                                                                                    │
│                                                                                                  │
│   136 │   │                                                                                      │
│   137 │   │   if self.component_type == "modules":                                               │
│   138 │   │   │   # Try to find a bioconda package for 'component'                               │
│ ❱ 139 │   │   │   self._get_bioconda_tool()                                                      │
│   140 │   │                                                                                      │
│   141 │   │   # Prompt for GitHub username                                                       │
│   142 │   │   self._get_username()                                                               │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/components/create.py: │
│ 227 in _get_bioconda_tool                                                                        │
│                                                                                                  │
│   224 │   │   │   │   │   │   self.tool_conda_name, version                                      │
│   225 │   │   │   │   │   )                                                                      │
│   226 │   │   │   │   else:                                                                      │
│ ❱ 227 │   │   │   │   │   self.docker_container, self.singularity_container = nf_core.utils.ge   │
│   228 │   │   │   │   │   │   self.component, version                                            │
│   229 │   │   │   │   │   )                                                                      │
│   230 │   │   │   │   log.info(f"Using Docker container: '{self.docker_container}'")             │
│                                                                                                  │
│ /home/noronhaa/anaconda3/envs/nf-core/lib/python3.10/site-packages/nf_core/utils.py:744 in       │
│ get_biocontainer_tag                                                                             │
│                                                                                                  │
│    741 │   │   │   │   │   │   singularity_image = all_singularity[k]["image"]                   │
│    742 │   │   │   │   │   │   current_date = date                                               │
│    743 │   │   │   │   │   │   docker_image_name = docker_image["image_name"].lstrip("quay.io/"  │
│ ❱  744 │   │   │   │   return docker_image_name, singularity_image["image_name"]                 │
│    745 │   │   │   except TypeError:                                                             │
│    746 │   │   │   │   raise LookupError(f"Could not find docker or singularity container for {  │
│    747 │   │   elif response.status_code != 404:                                                 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
UnboundLocalError: local variable 'docker_image_name' referenced before assignment

System information

CentOSLinux, Python 3.10, nf-core version 2.9

[mirpedrol]

Hello @anoronh4, thanks for the detailed issue. This was fixed in the dev version by #2374
You can install the dev version of tools following these instructions