Hi all, I am getting this error when using

nf-core lint

and it seems related to the nf-core installation in a virtual environment:

/home/ubuntu/Projects/VENVS/nextflow-env/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/ubuntu/Projects/VENVS/nextflow-env/lib/python3.10/site-packages/nf_core/__main__.py:150 in │
│ run_nf_core                                                                                      │
│                                                                                                  │
│    147 │   │   │   log.debug(f"Could not check latest version: {e}")                             │
│    148 │   │   stderr.print("\n")                                                                │
│    149 │   # Launch the click cli                                                                │
│ ❱  150 │   nf_core_cli(auto_envvar_prefix="NFCORE")                                              │
│    151                                                                                           │
│    152                                                                                           │
│    153 @tui()                                                                                    │
│                                                                                                  │
│ /home/ubuntu/Projects/VENVS/nextflow-env/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):                                 │
│                                                                                                  │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ValueError: not enough values to unpack (expected 2, got 1)

Did anyone experience a similar issue? Maybe I am not applying the lint command properly? Thanks! P.S. I couldn't paste the whole error due to characters limitation, but happy to provide the entire one separately

If you could provide the entire output as a Slack snippet, that'd be great

Thanks Phil, I forgot about the snippet option! Here is the whole error. I am working on a custom pipeline based on the Sarek workflow. I cloned the Sarek repo almost a year ago but I have never actually tried the linting command so I am wondering if this is the problem? It looks like a python issue related to venv. Any insights? Thanks!

Thanks! Still missing the top of the stdout though, saying what version you're running of #CE5LG7WMB and what the command was to launch it

Sorry, my bad! Here is the full output

It looks like it's throwing an error when trying to do something with the pipeline config