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nf-core install could not detect work dir
Have you checked the docs?
Description of the bug
I want to add the module trimgalore into my workflow. However, the command nf-core modules install trimgalore --dir $PWD returned me error saying PermissionError: [Errno 13] Permission denied: '/.nf-core.yml'. It seems like it could not solve the workding directory and tried to modify the root directory /.
PS: Removing --dir $PWD did not solve the problem.
Command used and terminal output
$echo $PWD
/weka/dhe/projects/discovery_seq_analysis
$ nf-core modules install trimgalore --dir $PWD
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.14.1 - https://nf-co.re
WARNING 'repository_type' not defined in .nf-core.yml
? Is this repository an nf-core pipeline or a fork of nf-core/modules? Pipeline
INFO To avoid this prompt in the future, add the 'repository_type' key to your .nf-core.yml file.
? Would you like me to add this config now? [y/n] (y):
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /usr/conda/envs/nf-core/bin/nf-core:10 in <module> │
│ │
│ 7 │
│ 8 if __name__ == '__main__': │
│ 9 │ sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) │
│ ❱ 10 │ sys.exit(run_nf_core()) │
│ 11 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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() │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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): │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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): │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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! │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/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 │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/__main__.py:839 in modules_install │
│ │
│ 836 │ from nf_core.modules import ModuleInstall │
│ 837 │ │
│ 838 │ try: │
│ ❱ 839 │ │ module_install = ModuleInstall( │
│ 840 │ │ │ dir, │
│ 841 │ │ │ force, │
│ 842 │ │ │ prompt, │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/modules/install.py:16 in __init__ │
│ │
│ 13 │ │ no_pull=False, │
│ 14 │ │ installed_by=False, │
│ 15 │ ): │
│ ❱ 16 │ │ super().__init__( │
│ 17 │ │ │ pipeline_dir, │
│ 18 │ │ │ "modules", │
│ 19 │ │ │ force=force, │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/components/install.py:35 in │
│ __init__ │
│ │
│ 32 │ │ no_pull=False, │
│ 33 │ │ installed_by=False, │
│ 34 │ ): │
│ ❱ 35 │ │ super().__init__(component_type, pipeline_dir, remote_url, branch, no_pull) │
│ 36 │ │ self.force = force │
│ 37 │ │ self.prompt = prompt │
│ 38 │ │ self.sha = sha │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/components/components_command.py:40 │
│ in __init__ │
│ │
│ 37 │ │ self.modules_repo = ModulesRepo(remote_url, branch, no_pull, hide_progress) │
│ 38 │ │ self.hide_progress = hide_progress │
│ 39 │ │ self.no_prompts = no_prompts │
│ ❱ 40 │ │ self._configure_repo_and_paths() │
│ 41 │ │
│ 42 │ def _configure_repo_and_paths(self, nf_dir_req: bool = True) -> None: │
│ 43 │ │ """ │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/components/components_command.py:53 │
│ in _configure_repo_and_paths │
│ │
│ 50 │ │ │
│ 51 │ │ try: │
│ 52 │ │ │ if self.dir: │
│ ❱ 53 │ │ │ │ self.dir, self.repo_type, self.org = get_repo_info(self.dir, use_prompt= │
│ 54 │ │ │ else: │
│ 55 │ │ │ │ self.repo_type = None │
│ 56 │ │ │ │ self.org = "" │
│ │
│ /usr/conda/envs/nf-core/lib/python3.12/site-packages/nf_core/components/components_utils.py:47 │
│ in get_repo_info │
│ │
│ 44 │ │ # Save the choice in the config file │
│ 45 │ │ log.info(f"To avoid this prompt in the future, add the 'repository_type' key to │
│ 46 │ │ if rich.prompt.Confirm.ask("[bold][blue]?[/] Would you like me to add this confi │
│ ❱ 47 │ │ │ with open(config_fn, "a+") as fh: │
│ 48 │ │ │ │ fh.write(f"repository_type: {repo_type}\n") │
│ 49 │ │ │ │ log.info(f"Config added to '{config_fn.name}'") │
│ 50 │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
PermissionError: [Errno 13] Permission denied: '/.nf-core.yml'
Relevant files
N/A
System information
nf-core, version 2.14.1
nextflow version 24.04.4.5917
Hardware: An AWS instance
executor: local
$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.5 LTS
Release: 22.04
Codename: jammy
