I recently ran into a weird issue with pipeline linting while doing other Git-related pipeline work, and I must have somehow messed up the local clone of ~/.config/nfcore/nf-core/modules. I asked in Slack and the problem was easily solved by removing this directory and allowing the linting to re-download it, but I was asked to create an issue for getting a more informative error message; see the Slack conversation here: https://nfcore.slack.com/archives/CJRH30T6V/p1730226056665409.
Since the issue was so simple to solve, I think the problem here was that I was not even aware that ~/.config/nfcore/nf-core/modules was a possible location for nf-core files to live in - I was troubleshooting and looking into tmp files and such. Maybe I should have known this, though (it's probably in the documentation somewhere?).
Command used and terminal output
$ nf-core pipelines lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 3.0.2 - https://nf-co.re
INFO Testing pipeline: .
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /Library/Frameworks/Python.framework/Versions/3.12/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 │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/__main__ │
│ .py:180 in run_nf_core │
│ │
│ 177 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 178 │ │ stderr.print("\n") │
│ 179 │ # Launch the click cli │
│ ❱ 180 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 181 │
│ 182 │
│ 183 @tui( │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/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): │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/click/core.py:11 │
│ 57 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): │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/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! │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/click/core.py:16 │
│ 88 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 │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/click/core.py:16 │
│ 88 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 │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/click/core.py:14 │
│ 34 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 │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/click/core.py:78 │
│ 3 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 │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/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 │
│ │
NEW
19:23
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/__main__ │
│ .py:349 in command_pipelines_lint │
│ │
│ 346 │ """ │
│ 347 │ Check pipeline code against nf-core guidelines. │
│ 348 │ """ │
│ ❱ 349 │ pipelines_lint(ctx, directory, release, fix, key, show_passed, fail_ignored, fail_wa │
│ 350 │
│ 351 │
│ 352 # nf-core pipelines download │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/commands │
│ _pipelines.py:133 in pipelines_lint │
│ │
│ 130 │ │
│ 131 │ # Run the lint tests! │
│ 132 │ try: │
│ ❱ 133 │ │ lint_obj, module_lint_obj, subworkflow_lint_obj = run_linting( │
│ 134 │ │ │ directory, │
│ 135 │ │ │ release, │
│ 136 │ │ │ fix, │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/pipeline │
│ s/lint/__init__.py:650 in run_linting │
│ │
│ 647 │ │ if len(module_lint_obj.all_local_components) > 0: │
│ 648 │ │ │ module_lint_obj.lint_modules(module_lint_obj.all_local_components, local=Tru │
│ 649 │ │ if len(module_lint_obj.all_remote_components) > 0: │
│ ❱ 650 │ │ │ module_lint_obj.lint_modules(module_lint_obj.all_remote_components, local=Fa │
│ 651 │ if subworkflow_lint_obj is not None: │
│ 652 │ │ # Run the subworkflows lint tests │
│ 653 │ │ if len(subworkflow_lint_obj.all_local_components) > 0: │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/modules/ │
│ lint/__init__.py:210 in lint_modules │
│ │
│ 207 │ │ │ │
│ 208 │ │ │ for mod in modules: │
│ 209 │ │ │ │ progress_bar.update(lint_progress, advance=1, test_name=mod.component_na │
│ ❱ 210 │ │ │ │ self.lint_module(mod, progress_bar, local=local, fix_version=fix_version │
│ 211 │ │
│ 212 │ def lint_module( │
│ 213 │ │ self, │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/modules/ │
│ lint/__init__.py:262 in lint_module │
│ │
│ 259 │ │ │ │ if test_name == "main_nf": │
│ 260 │ │ │ │ │ getattr(self, test_name)(mod, fix_version, self.registry, progress_b │
│ 261 │ │ │ │ else: │
│ ❱ 262 │ │ │ │ │ getattr(self, test_name)(mod) │
│ 263 │ │ │ │
│ 264 │ │ │ self.passed += [LintResult(mod, *m) for m in mod.passed] │
│ 265 │ │ │ warned = [LintResult(mod, *m) for m in mod.warned] │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/modules/ │
│ lint/module_changes.py:53 in module_changes │
│ │
│ 50 │ ) │
│ 51 │ modules_repo = nf_core.modules.modules_repo.ModulesRepo(remote_url=module.repo_url, │
│ 52 │ │
│ ❱ 53 │ for f, same in modules_repo.component_files_identical( │
│ 54 │ │ module.component_name, tempdir, module.git_sha, "modules" │
│ 55 │ ).items(): │
│ 56 │ │ if same: │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/synced_r │
│ epo.py:342 in component_files_identical │
│ │
│ 339 │ │ if commit is None: │
│ 340 │ │ │ self.checkout_branch() │
│ 341 │ │ else: │
│ ❱ 342 │ │ │ self.checkout(commit) │
│ 343 │ │ component_files = ["main.nf", "meta.yml"] │
│ 344 │ │ files_identical = {file: True for file in component_files} │
│ 345 │ │ component_dir = self.get_component_dir(component_name, component_type) │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/synced_r │
│ epo.py:263 in checkout │
│ │
19:23
│ 260 │ │ │ │ log.debug(f"Overwriting local changes in '{self.local_repo_dir}'") │
│ 261 │ │ │ │ self.repo.git.checkout(self.branch, force=True) │
│ 262 │ │ │ else: │
│ ❱ 263 │ │ │ │ raise e │
│ 264 │ │
│ 265 │ def component_exists(self, component_name, component_type, checkout=True, commit=Non │
│ 266 │ │ """ │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nf_core/synced_r │
│ epo.py:253 in checkout │
│ │
│ 250 │ │ │ commit (str): Git SHA of the commit │
│ 251 │ │ """ │
│ 252 │ │ try: │
│ ❱ 253 │ │ │ self.repo.git.checkout(commit) │
│ 254 │ │ except GitCommandError as e: │
│ 255 │ │ │ if ( │
│ 256 │ │ │ │ self.fullname │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/git/cmd.py:736 │
│ in <lambda> │
│ │
│ 733 │ │ :return: Callable object that will execute call _call_process with your argument │
│ 734 │ │ if name[0] == "_": │
│ 735 │ │ │ return LazyMixin.__getattr__(self, name) │
│ ❱ 736 │ │ return lambda *args, **kwargs: self._call_process(name, *args, **kwargs) │
│ 737 │ │
│ 738 │ def set_persistent_git_options(self, **kwargs: Any) -> None: │
│ 739 │ │ """Specify command line options to the git executable │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/git/cmd.py:1316 │
│ in _call_process │
│ │
│ 1313 │ │ call.append(dashify(method)) │
│ 1314 │ │ call.extend(args_list) │
│ 1315 │ │ │
│ ❱ 1316 │ │ return self.execute(call, **exec_kwargs) │
│ 1317 │ │
│ 1318 │ def _parse_object_header(self, header_line: str) -> Tuple[str, str, int]: │
│ 1319 │ │ """ │
│ │
│ /Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/git/cmd.py:1111 │
│ in execute │
│ │
│ 1108 │ │ # END handle debug printing │
│ 1109 │ │ │
│ 1110 │ │ if with_exceptions and status != 0: │
│ ❱ 1111 │ │ │ raise GitCommandError(redacted_command, status, stderr_value, stdout_value) │
│ 1112 │ │ │
│ 1113 │ │ if isinstance(stdout_value, bytes) and stdout_as_string: # could also be output │
│ 1114 │ │ │ stdout_value = safe_decode(stdout_value) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git checkout 06c8865e36741e05ad32ef70ab3fac127486af48
stderr: 'error: The following untracked working tree files would be overwritten by checkout:
modules/nf-core/bismark/align/tests/nextflow_bowtie2.config
modules/nf-core/bismark/align/tests/nextflow_hisat2.config
modules/nf-core/bismark/align/tests/nextflow_minimap2.config
modules/nf-core/bismark/align/tests/tags.yml
modules/nf-core/bismark/coverage2cytosine/tests/tags.yml
modules/nf-core/bismark/deduplicate/tests/tags.yml
modules/nf-core/bismark/genomepreparation/tests/tags.yml
modules/nf-core/bismark/methylationextractor/tests/tags.yml
modules/nf-core/bismark/report/tests/tags.yml
modules/nf-core/bismark/summary/tests/tags.yml
modules/nf-core/deepvariant/tests/main.nf.test.snap
modules/nf-core/deepvariant/tests/nextflow-intervals.config
modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config
modules/nf-core/deepvariant/tests/nextflow.config
modules/nf-core/flye/tests/nextflow.config
Please move or remove them before you switch branches.
Aborting'
Description of the bug
I recently ran into a weird issue with pipeline linting while doing other Git-related pipeline work, and I must have somehow messed up the local clone of
~/.config/nfcore/nf-core/modules. I asked in Slack and the problem was easily solved by removing this directory and allowing the linting to re-download it, but I was asked to create an issue for getting a more informative error message; see the Slack conversation here: https://nfcore.slack.com/archives/CJRH30T6V/p1730226056665409.Since the issue was so simple to solve, I think the problem here was that I was not even aware that
~/.config/nfcore/nf-core/moduleswas a possible location for nf-core files to live in - I was troubleshooting and looking into tmp files and such. Maybe I should have known this, though (it's probably in the documentation somewhere?).Command used and terminal output
System information
No response