Closed Ethan-Hetrick closed 2 months ago
arunbodd
commented
8 months ago I too have received a similar error while installing a module. Its an anomaly that if I re-try module install, it outputs the above error message but installs the module in modules/ folder.
Ethan-Hetrick
commented
8 months ago Update: Folks in the Slack channel asked me to clear my nf-core cache and try again -- this was still unsuccessful
mashehu
commented
8 months ago Sorry, I tried it and couldn't reproduce this (using the same python version etc.). the error indicating that tests/modules/nf-core/hisat2/build has changes in it, sounds to me that is not really related to the install command. could you rm -rf ~/.config/nfcore/nf-core/modules/ and then retry the commands above.
Ethan-Hetrick
commented
8 months ago I tried that, gave me the same error.
mashehu
commented
8 months ago hmm. Can you run nf-core --verbose modules install quast and post the output here, so we can get a bit more debugging info?
mashehu
commented
8 months ago and also post your values for $XDG_CONFIG_HOME and $HOME
Ethan-Hetrick
commented
8 months ago # Remove cache
$ rm -rf ~/.config/nfcore/nf-core/modules/
$ rm -rf ~/.nfcore/
$ rm -rf ~/.nextflow/nf-core
# Install quast
$ nf-core --verbose modules install quast
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.1 - https://nf-co.re
Pulling from 'nf-core/modules' (https://github.com/nf-core/modules.git) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG Popen(['git', 'version'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, cmd.py:1057
stdin=None, shell=False, universal_newlines=True)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, cmd.py:1057
shell=False, universal_newlines=False)
DEBUG Using config file: /scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1034
DEBUG Using config file: .nf-core.yml utils.py:1034
DEBUG Popen(['git', 'checkout', 'master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=<valid cmd.py:1057
stream>, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'rev-list', '--max-count=1', 'd6a146325058eb9a18da2e898a2376e1d1093052', '--', 'modules/nf-core/quast'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=<valid stream>, cmd.py:1057
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'rev-list', '--max-count=1', 'd6a146325058eb9a18da2e898a2376e1d1093052', '--', 'modules/quast'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
INFO Installing 'quast' install.py:110
DEBUG Installing modules 'quast' at modules hash 3f5420aa22e00bd030a2556dfdffc9e164ec0ec5 from install.py:111
https://github.com/nf-core/modules.git
DEBUG Popen(['git', 'checkout', '3f5420aa22e00bd030a2556dfdffc9e164ec0ec5'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False, cmd.py:1057
universal_newlines=False)
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/__mai │
│ n__.py:111 in run_nf_core │
│ │
│ 108 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 109 │ │ stderr.print("\n") │
│ 110 │ # Launch the click cli │
│ ❱ 111 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 112 │
│ 113 │
│ 114 @click.group(context_settings=dict(help_option_names=["-h", "--help"])) │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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): │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/rich_click/ri │
│ ch_command.py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(ctx) │
│ 127 │ │ │ │ │ if not standalone_mode: │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/click/decorat │
│ ors.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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/__mai │
│ n__.py:654 in modules_install │
│ │
│ 651 │ │ │ ctx.obj["modules_repo_branch"], │
│ 652 │ │ │ ctx.obj["modules_repo_no_pull"], │
│ 653 │ │ ) │
│ ❱ 654 │ │ exit_status = module_install.install(tool) │
│ 655 │ │ if not exit_status: │
│ 656 │ │ │ sys.exit(1) │
│ 657 │ except (UserWarning, LookupError) as e: │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/compo │
│ nents/install.py:116 in install │
│ │
│ 113 │ │ ) │
│ 114 │ │ │
│ 115 │ │ # Download component files │
│ ❱ 116 │ │ if not self.install_component_files(component, version, self.modules_repo, insta │
│ 117 │ │ │ return False │
│ 118 │ │ │
│ 119 │ │ # Update module.json with newly installed subworkflow │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/compo │
│ nents/components_command.py:173 in install_component_files │
│ │
│ 170 │ │ Returns: │
│ 171 │ │ │ (bool): Whether the operation was successful of not │
│ 172 │ │ """ │
│ ❱ 173 │ │ return modules_repo.install_component(component_name, install_dir, component_ver │
│ 174 │ │
│ 175 │ def load_lint_config(self) -> None: │
│ 176 │ │ """Parse a pipeline lint config file. │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/synce │
│ d_repo.py:281 in install_component │
│ │
│ 278 │ │ shutil.copytree(self.get_component_dir(component_name, component_type), Path(ins │
│ 279 │ │ │
│ 280 │ │ # Switch back to the tip of the branch │
│ ❱ 281 │ │ self.checkout_branch() │
│ 282 │ │ return True │
│ 283 │ │
│ 284 │ def component_files_identical(self, component_name, base_path, commit, component_typ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/synce │
│ d_repo.py:214 in checkout_branch │
│ │
│ 211 │ │ """ │
│ 212 │ │ Checks out the specified branch of the repository │
│ 213 │ │ """ │
│ ❱ 214 │ │ self.repo.git.checkout(self.branch) │
│ 215 │ │
│ 216 │ def checkout(self, commit): │
│ 217 │ │ """ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:80 │
│ 0 in <lambda> │
│ │
│ 797 │ │ """ │
│ 798 │ │ if name[0] == "_": │
│ 799 │ │ │ return LazyMixin.__getattr__(self, name) │
│ ❱ 800 │ │ return lambda *args, **kwargs: self._call_process(name, *args, **kwargs) │
│ 801 │ │
│ 802 │ def set_persistent_git_options(self, **kwargs: Any) -> None: │
│ 803 │ │ """Specify command line options to the git executable for subsequent │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:13 │
│ 86 in _call_process │
│ │
│ 1383 │ │ call.append(dashify(method)) │
│ 1384 │ │ call.extend(args_list) │
│ 1385 │ │ │
│ ❱ 1386 │ │ return self.execute(call, **exec_kwargs) │
│ 1387 │ │
│ 1388 │ def _parse_object_header(self, header_line: str) -> Tuple[str, str, int]: │
│ 1389 │ │ """ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:11 │
│ 83 in execute │
│ │
│ 1180 │ │ # END handle debug printing │
│ 1181 │ │ │
│ 1182 │ │ if with_exceptions and status != 0: │
│ ❱ 1183 │ │ │ raise GitCommandError(redacted_command, status, stderr_value, stdout_value) │
│ 1184 │ │ │
│ 1185 │ │ if isinstance(stdout_value, bytes) and stdout_as_string: # Could also be output │
│ 1186 │ │ │ stdout_value = safe_decode(stdout_value) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git checkout master
stderr: 'error: Your local changes to the following files would be overwritten by checkout:
tests/modules/nf-core/hisat2/build
Please commit your changes or stash them before you switch branches.
Aborting'
# Print contents of config files
$ cat ~/.config/nfcore/nf-core/modules/.nf-core.yml
repository_type: modules
org_path: nf-core
bump-versions:
rseqc/junctionannotation: False
rseqc/bamstat: False
rseqc/readduplication: False
rseqc/readdistribution: False
rseqc/junctionsaturation: False
rseqc/inferexperiment: False
rseqc/innerdistance: False
sortmerna: False
$ cat ./.nf-core.yml
repository_type: modules
org_path: nf-core
bump-versions:
rseqc/junctionannotation: False
rseqc/bamstat: False
rseqc/readduplication: False
rseqc/readdistribution: False
rseqc/junctionsaturation: False
rseqc/inferexperiment: False
rseqc/innerdistance: False
sortmerna: False
(/scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore) Ethan from SciComp @node235 :~/TRAINING/build_nextflow_pipeline_seminar_01_10_2024/test-test$ cat ./.nf-core.yml
lint:
files_exist:
- CODE_OF_CONDUCT.md
- assets/nf-core-test_logo_light.png
- docs/images/nf-core-test_logo_light.png
- docs/images/nf-core-test_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- .github/ISSUE_TEMPLATE/bug_report.yml
- .github/ISSUE_TEMPLATE/feature_request.yml
- .github/PULL_REQUEST_TEMPLATE.md
- .github/CONTRIBUTING.md
- .github/.dockstore.yml
- .gitignore
- .github/workflows/branch.yml
- .github/workflows/ci.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- conf/igenomes.config
- conf/igenomes.config
files_unchanged:
- CODE_OF_CONDUCT.md
- assets/nf-core-test_logo_light.png
- docs/images/nf-core-test_logo_light.png
- docs/images/nf-core-test_logo_dark.png
- .github/ISSUE_TEMPLATE/bug_report.yml
- .github/ISSUE_TEMPLATE/config.yml
- .github/ISSUE_TEMPLATE/feature_request.yml
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- .github/CONTRIBUTING.md
- .github/.dockstore.yml
- .github/ISSUE_TEMPLATE/bug_report.yml
multiqc_config:
- report_comment
nextflow_config:
- manifest.name
- manifest.homePage
- process.cpus
- process.memory
- process.time
- custom_config
readme:
- nextflow_badge
repository_type: pipeline
template:
prefix: test
skip:
- github
- ci
- github_badges
- igenomes
- nf_core_configs
# Output versions
$ nextflow -version
N E X T F L O W
version 23.10.1 build 5891
created 12-01-2024 22:01 UTC (17:01 EDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
$ nf-core --version
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.11.1 - https://nf-co.re
nf-core, version 2.11.1
# Print out environment variables
# Printed nothing
# Tried `export XDG_CONFIG_HOME="$HOME/.config"` before running nf-core, no change
$ echo $XDG_CONFIG_HOME
$ echo $HOME
/scicomp/home-pure/rqu4We went ahead and updated our version of git on our cluster, and I also went ahead and got the latest releases of nf-core tools and nextflow as well. It gave me a similar error, however now it is saying malt is the issue instead of hisat2.
$ nextflow -version
N E X T F L O W
version 23.10.1 build 5891
created 12-01-2024 22:01 UTC (17:01 EDT)
cite doi:10.1038/nbt.3820
http://nextflow.io
$ nf-core --version
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.12.1 - https://nf-co.re
nf-core, version 2.12.1
$ git --version
git version 2.43.0
$ rm -rf ~/.config/nfcore/nf-core/modules/
$ rm -rf ~/.nfcore/
$ rm -rf ~/.nextflow/nf-core
$ nf-core --verbose modules install quast
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.12.1 - https://nf-co.re
Cloning from 'nf-core/modules' (https://github.com/nf-core/modules.git) ━━━━━━━━━━━━━━━━━━ Waiting for responseDEBUG Popen(['git', 'version'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/TRAINING/build_nextflow_pipeline_seminar_01_10_2024/test-test,
stdin=None, shell=False, universal_newlines=False)
DEBUG Popen(['git', 'clone', '-v', '--progress', '--', 'https://github.com/nf-core/modules.git', cmd.py:1057
'/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules'],
cwd=/scicomp/home-pure/rqu4/TRAINING/build_nextflow_pipeline_seminar_01_10_2024/test-test,
stdin=None, shell=False, universal_newlines=True)
DEBUG Popen(['git', 'checkout', 'master'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Using config file: /scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043
DEBUG Using config file: .nf-core.yml utils.py:1043
DEBUG Popen(['git', 'checkout', 'master'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch-check'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=<valid stream>,
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'rev-list', '--max-count=1', 'ce0b1aed7d504883061e748f492a31bf44c5777c', cmd.py:1057
'--', 'modules/nf-core/quast'],
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Popen(['git', 'cat-file', '--batch'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=<valid stream>,
shell=False, universal_newlines=False)
DEBUG Popen(['git', 'rev-list', '--max-count=1', 'ce0b1aed7d504883061e748f492a31bf44c5777c', cmd.py:1057
'--', 'modules/quast'], cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules,
stdin=None, shell=False, universal_newlines=False)
INFO Installing 'quast' install.py:110
DEBUG Installing modules 'quast' at modules hash 3f5420aa22e00bd030a2556dfdffc9e164ec0ec5 install.py:111
from https://github.com/nf-core/modules.git
DEBUG Popen(['git', 'checkout', '3f5420aa22e00bd030a2556dfdffc9e164ec0ec5'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
DEBUG Popen(['git', 'checkout', 'master'], cmd.py:1057
cwd=/scicomp/home-pure/rqu4/.config/nfcore/nf-core/modules, stdin=None, shell=False,
universal_newlines=False)
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/__mai │
│ n__.py:141 in run_nf_core │
│ │
│ 138 │ │ │ log.debug(f"Could not check latest version: {e}") │
│ 139 │ │ stderr.print("\n") │
│ 140 │ # Launch the click cli │
│ ❱ 141 │ nf_core_cli(auto_envvar_prefix="NFCORE") │
│ 142 │
│ 143 │
│ 144 @tui() │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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): │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/rich_click/ri │
│ ch_command.py:126 in main │
│ │
│ 123 │ │ try: │
│ 124 │ │ │ try: │
│ 125 │ │ │ │ with self.make_context(prog_name, args, **extra) as ctx: │
│ ❱ 126 │ │ │ │ │ rv = self.invoke(ctx) │
│ 127 │ │ │ │ │ if not standalone_mode: │
│ 128 │ │ │ │ │ │ return rv │
│ 129 │ │ │ │ │ # it's not safe to `ctx.exit(rv)` here! │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/click/decorat │
│ ors.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 │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/__mai │
│ n__.py:820 in modules_install │
│ │
│ 817 │ │ │ ctx.obj["modules_repo_branch"], │
│ 818 │ │ │ ctx.obj["modules_repo_no_pull"], │
│ 819 │ │ ) │
│ ❱ 820 │ │ exit_status = module_install.install(tool) │
│ 821 │ │ if not exit_status: │
│ 822 │ │ │ sys.exit(1) │
│ 823 │ except (UserWarning, LookupError) as e: │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/compo │
│ nents/install.py:116 in install │
│ │
│ 113 │ │ ) │
│ 114 │ │ │
│ 115 │ │ # Download component files │
│ ❱ 116 │ │ if not self.install_component_files(component, version, self.modules_repo, insta │
│ 117 │ │ │ return False │
│ 118 │ │ │
│ 119 │ │ # Update module.json with newly installed subworkflow │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/compo │
│ nents/components_command.py:173 in install_component_files │
│ │
│ 170 │ │ Returns: │
│ 171 │ │ │ (bool): Whether the operation was successful of not │
│ 172 │ │ """ │
│ ❱ 173 │ │ return modules_repo.install_component(component_name, install_dir, component_ver │
│ 174 │ │
│ 175 │ def load_lint_config(self) -> None: │
│ 176 │ │ """Parse a pipeline lint config file. │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/synce │
│ d_repo.py:278 in install_component │
│ │
│ 275 │ │ shutil.copytree(self.get_component_dir(component_name, component_type), Path(ins │
│ 276 │ │ │
│ 277 │ │ # Switch back to the tip of the branch │
│ ❱ 278 │ │ self.checkout_branch() │
│ 279 │ │ return True │
│ 280 │ │
│ 281 │ def component_files_identical(self, component_name, base_path, commit, component_typ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/nf_core/synce │
│ d_repo.py:211 in checkout_branch │
│ │
│ 208 │ │ """ │
│ 209 │ │ Checks out the specified branch of the repository │
│ 210 │ │ """ │
│ ❱ 211 │ │ self.repo.git.checkout(self.branch) │
│ 212 │ │
│ 213 │ def checkout(self, commit): │
│ 214 │ │ """ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:80 │
│ 0 in <lambda> │
│ │
│ 797 │ │ """ │
│ 798 │ │ if name[0] == "_": │
│ 799 │ │ │ return LazyMixin.__getattr__(self, name) │
│ ❱ 800 │ │ return lambda *args, **kwargs: self._call_process(name, *args, **kwargs) │
│ 801 │ │
│ 802 │ def set_persistent_git_options(self, **kwargs: Any) -> None: │
│ 803 │ │ """Specify command line options to the git executable for subsequent │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:13 │
│ 86 in _call_process │
│ │
│ 1383 │ │ call.append(dashify(method)) │
│ 1384 │ │ call.extend(args_list) │
│ 1385 │ │ │
│ ❱ 1386 │ │ return self.execute(call, **exec_kwargs) │
│ 1387 │ │
│ 1388 │ def _parse_object_header(self, header_line: str) -> Tuple[str, str, int]: │
│ 1389 │ │ """ │
│ │
│ /scicomp/home-pure/rqu4/my_conda_envs/nextflow_nfcore/lib/python3.12/site-packages/git/cmd.py:11 │
│ 83 in execute │
│ │
│ 1180 │ │ # END handle debug printing │
│ 1181 │ │ │
│ 1182 │ │ if with_exceptions and status != 0: │
│ ❱ 1183 │ │ │ raise GitCommandError(redacted_command, status, stderr_value, stdout_value) │
│ 1184 │ │ │
│ 1185 │ │ if isinstance(stdout_value, bytes) and stdout_as_string: # Could also be output │
│ 1186 │ │ │ stdout_value = safe_decode(stdout_value) │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git checkout master
stderr: 'error: Your local changes to the following files would be overwritten by checkout:
tests/modules/nf-core/malt/build
Please commit your changes or stash them before you switch branches.
Aborting'I also tried to not customize the nf-core template at all and got a similar error, however now it is complaining about both hisat2 and malt
GitCommandError: Cmd('git') failed due to: exit code(1)
cmdline: git checkout master
stderr: 'error: Your local changes to the following files would be overwritten by checkout:
tests/modules/nf-core/hisat2/build
tests/modules/nf-core/malt/build
Please commit your changes or stash them before you switch branches.
Aborting'This issue can probably be closed as this does not occur with recent versions of nf-core
Description of the bug
When using
nf-core modules installwith any module, I get the following Git error. However, it seems that the command works and the files are placed as normal where they should be. I am confused as to why it outputs something about the hisat2 module, as that is not the module I am installing. This was tested on nf-core/2.11.1 and replicated on v.2.10 as well. For context, this is in a fresh Conda environment and I had 10+ users experience this same issue on various environments. I do know that the version of Git on this HPC system is ancient and could be due to that. The question is, what versions of Git are compatible and is that even the cause of this error?Command used and terminal output
System information
No response