nf-core list throws InvalidGitRepositoryError error

[mahesh-panchal]

Description of the bug

nf-core list throws an InvalidGitRepositoryError:/home/mahesh/.nextflow/assets/NBISweden/pipelines-nextflow.
It's looking at the wrong folder for the nf-core assets.

$ ls /home/mahesh/.nextflow/assets/
ewels  NBISweden  nextflow-io  nf-core

Steps to reproduce

Steps to reproduce the behaviour:

1. conda activate nextflow-env ( has nf-core 2.1 installed, along with nextflow, mamba, and pandoc ).

2. nf-core list

3. See error:

$ nf-core list

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

    nf-core/tools version 2.1



╭───────────────────────────────────────────────────── Traceback (most recent call last) ─────────────────────────────────────────────────────╮
│ /home/mahesh/.conda/envs/nextflow-env/bin/nf-core:10 in <module>                                                                            │
│                                                                                                                                             │
│    9 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                                                                   │
│ ❱ 10 │   sys.exit(run_nf_core())                                                                                                            │
│   11                                                                                                                                        │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/nf_core/__main__.py:62 in run_nf_core                                     │
│                                                                                                                                             │
│    61 │   # Lanch the click cli                                                                                                             │
│ ❱  62 │   nf_core_cli()                                                                                                                     │
│    63                                                                                                                                       │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/click/core.py:1134 in __call__                                            │
│                                                                                                                                             │
│   1133 │   │   """Alias for :meth:`main`."""                                                                                                │
│ ❱ 1134 │   │   return self.main(*args, **kwargs)                                                                                            │
│   1135                                                                                                                                      │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/click/core.py:1059 in main                                                │
│                                                                                                                                             │
│   1058 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                                                             │
│ ❱ 1059 │   │   │   │   │   rv = self.invoke(ctx)                                                                                            │
│   1060 │   │   │   │   │   if not standalone_mode:                                                                                          │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/click/core.py:1665 in invoke                                              │
│                                                                                                                                             │
│   1664 │   │   │   │   with sub_ctx:                                                                                                        │
│ ❱ 1665 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))                                                          │
│   1666                                                                                                                                      │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/click/core.py:1401 in invoke                                              │
│                                                                                                                                             │
│   1400 │   │   if self.callback is not None:                                                                                                │
│ ❱ 1401 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                                                           │
│   1402                                                                                                                                      │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/click/core.py:767 in invoke                                               │
│                                                                                                                                             │
│    766 │   │   │   with ctx:                                                                                                                │
│ ❱  767 │   │   │   │   return __callback(*args, **kwargs)                                                                                   │
│    768                                                                                                                                      │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/nf_core/__main__.py:156 in list                                           │
│                                                                                                                                             │
│   155 │   """                                                                                                                               │
│ ❱ 156 │   print(nf_core.list.list_workflows(keywords, sort, json, show_archived))                                                           │
│   157                                                                                                                                       │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/nf_core/list.py:36 in list_workflows                                      │
│                                                                                                                                             │
│    35 │   wfs.get_remote_workflows()                                                                                                        │
│ ❱  36 │   wfs.get_local_nf_workflows()                                                                                                      │
│    37 │   wfs.compare_remote_local()                                                                                                        │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/nf_core/list.py:142 in get_local_nf_workflows                             │
│                                                                                                                                             │
│   141 │   │   for wf in self.local_workflows:                                                                                               │
│ ❱ 142 │   │   │   wf.get_local_nf_workflow_details()                                                                                        │
│   143                                                                                                                                       │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/nf_core/list.py:357 in get_local_nf_workflow_details                      │
│                                                                                                                                             │
│   356 │   │   │   try:                                                                                                                      │
│ ❱ 357 │   │   │   │   repo = git.Repo(self.local_path)                                                                                      │
│   358 │   │   │   │   self.commit_sha = str(repo.head.commit.hexsha)                                                                        │
│                                                                                                                                             │
│ /home/mahesh/.conda/envs/nextflow-env/lib/python3.7/site-packages/git/repo/base.py:198 in __init__                                          │
│                                                                                                                                             │
│    197 │   │   │   self.git_dir = cast(PathLike, self.git_dir)                                                                              │
│ ❱  198 │   │   │   raise InvalidGitRepositoryError(epath)                                                                                   │
│    199                                                                                                                                      │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
InvalidGitRepositoryError: /home/mahesh/.nextflow/assets/NBISweden/pipelines-nextflow

Expected behaviour

List nf-core workflows.
To only check the nf-core assets and not any others.

System

• Hardware: HPC, Laptop
• OS: Linux, macOS
• Version of nf-core/tools: 2.1
• Python version: 3.7.10

[ewels]

So after some Slack debugging with @mahesh-panchal we figured out that this path contains a broken repo clone somehow. Indeed, nf-core list crashes with this error if it encounters a path in the Nextflow assets folders that isn't a repo.

This basically shouldn't ever happen, as these assets directories are generated by Nextflow pulling a repo. However, it would still be nice to handle the error in a better way if it does instead of giving a huge traceback.