Better error message when user naively uses modules without having a pipeline
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@krokicki is already working on this.
Since Dec 11, 2023.
enhancement
- Dominant language
- Python
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- Merged PRs (30d)
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Description
Description of feature
Dear nf-core maintainer,
Here I suggest a feature that would guide new users into using modules, by giving a better error message. I do volunteer to add it via a PR, as I am quite interested in Nexflow and nf-core. Here is the feature request:
When one asks the info of a specific module...
nf-core modules info raxmlng
One gets some useful output, even with an install command:
Installation command: nf-core modules install raxmlng
Up until now, it has been smooth sailing.
However, when naively running that install command, the user will get an unhelpful error (see full error below): `PermissionError: [Errno 13] Permission denied: '/.nf-core.yml'.
The real error is that the command nf-core modules install [some module] can only be run within an existing pipeline (e.g. a naive touch .nf-core.yml does not solve the problem). Therefore, I suggest the error message to become this instead:
Cannot find '.nf-core.yml'.
Tip: a module must be installed as part of a pipeline. Use 'nf-core create' to start creating a pipeline'
Full error
(base) richel@richel-N141CU:~$ nf-core modules install raxmlng
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.7.2 - https://nf-co.re/
WARNING 'repository_type' not defined in .nf-core.yml
? Is this repository an nf-core pipeline or a fork of nf-core/modules? nf-core/modules
INFO To avoid this prompt in the future, add the 'repository_type' key to your
.nf-core.yml file.
? Would you like me to add this config now? [y/n] (y):
╭─────────────────────────── Traceback (most recent call last) ───────────────────────────╮
│ /home/richel/miniconda3/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/richel/miniconda3/lib/python3.10/site-packages/nf_core/__main__.py:105 in │
│ run_nf_core │
│ │
│ 104 │ # Launch the click cli │
│ ❱ 105 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 106 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:1130 in __call__ │
│ │
│ 1129 │ │ """Alias for :meth:`main`.""" │
│ ❱ 1130 │ │ return self.main(*args, **kwargs) │
│ 1131 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/rich_click/rich_group.py:21 in │
│ main │
│ │
│ 20 │ │ try: │
│ ❱ 21 │ │ │ rv = super().main(*args, standalone_mode=False, **kwargs) │
│ 22 │ │ │ if not standalone_mode: │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:1055 in main │
│ │
│ 1054 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 1055 │ │ │ │ │ rv = self.invoke(ctx) │
│ 1056 │ │ │ │ │ if not standalone_mode: │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:1657 in invoke │
│ │
│ 1656 │ │ │ │ with sub_ctx: │
│ ❱ 1657 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1658 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:1657 in invoke │
│ │
│ 1656 │ │ │ │ with sub_ctx: │
│ ❱ 1657 │ │ │ │ │ return _process_result(sub_ctx.command.invoke(sub_ctx)) │
│ 1658 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:1404 in invoke │
│ │
│ 1403 │ │ if self.callback is not None: │
│ ❱ 1404 │ │ │ return ctx.invoke(self.callback, **ctx.params) │
│ 1405 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/core.py:760 in invoke │
│ │
│ 759 │ │ │ with ctx: │
│ ❱ 760 │ │ │ │ return __callback(*args, **kwargs) │
│ 761 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/click/decorators.py:26 in new_func │
│ │
│ 25 │ def new_func(*args, **kwargs): # type: ignore │
│ ❱ 26 │ │ return f(get_current_context(), *args, **kwargs) │
│ 27 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/__main__.py:528 in install │
│ │
│ 527 │ try: │
│ ❱ 528 │ │ module_install = nf_core.modules.ModuleInstall( │
│ 529 │ │ │ dir, │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/modules/install.py:16 in │
│ __init__ │
│ │
│ 15 │ ): │
│ ❱ 16 │ │ super().__init__( │
│ 17 │ │ │ pipeline_dir, │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/components/install.py:36 │
│ in __init__ │
│ │
│ 35 │ ): │
│ ❱ 36 │ │ super().__init__(component_type, pipeline_dir, remote_url, branch, no_pul │
│ 37 │ │ self.force = force │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/components/components_comm │
│ and.py:30 in __init__ │
│ │
│ 29 │ │ self.hide_progress = hide_progress │
│ ❱ 30 │ │ self._configure_repo_and_paths() │
│ 31 │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/components/components_comm │
│ and.py:42 in _configure_repo_and_paths │
│ │
│ 41 │ │ │ if self.dir: │
│ ❱ 42 │ │ │ │ self.dir, self.repo_type, self.org = get_repo_info(self.dir, │
│ use_prompt=nf_dir_req) │
│ 43 │ │ │ else: │
│ │
│ /home/richel/miniconda3/lib/python3.10/site-packages/nf_core/components/components_util │
│ s.py:45 in get_repo_info │
│ │
│ 44 │ │ if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add thi │
│ config now?", default=True): │
│ ❱ 45 │ │ │ with open(config_fn, "a+") as fh: │
│ 46 │ │ │ │ fh.write(f"repository_type: {repo_type}\n") │
╰─────────────────────────────────────────────────────────────────────────────────────────╯
PermissionError: [Errno 13] Permission denied: '/.nf-core.yml'
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