I am unable to update a module with nf-core modules update, even if the module has been patched with nf-core modules patch if the change I introduce is a new file in the folder, such as a nextflow.config
It would be nice if I could update the modules without reinstalling them when I add files.
Command used and terminal output
$ tree modules/nf-core/multiqc
modules/nf-core/multiqc
├── environment.yml
├── main.nf
├── meta.yml
├── nextflow.config
└── tests
├── main.nf.test
├── main.nf.test.snap
└── tags.yml
$ nf-core modules patch multiqc
$ tree modules/nf-core/multiqc
modules/nf-core/multiqc
├── environment.yml
├── main.nf
├── meta.yml
├── multiqc.diff
├── nextflow.config
└── tests
├── main.nf.test
├── main.nf.test.snap
└── tags.yml
$ nf-core modules update multiqc
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.12.1 - https://nf-co.re
? Do you want to view diffs of the proposed changes? No previews, just update everything
INFO Found patch for module 'nf-core/multiqc'. Trying to apply it to new files
INFO Modules multiqc contains a patch file.
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/ec2-user/miniconda3/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/nf_core/__main__.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() │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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): │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/rich_click/rich_command.py:12 │
│ 6 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! │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/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 │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/nf_core/__main__.py:912 in │
│ modules_update │
│ │
│ 909 │ │ │ ctx.obj["modules_repo_branch"], │
│ 910 │ │ │ ctx.obj["modules_repo_no_pull"], │
│ 911 │ │ ) │
│ ❱ 912 │ │ exit_status = module_install.update(tool) │
│ 913 │ │ if not exit_status and install_all: │
│ 914 │ │ │ sys.exit(1) │
│ 915 │ except (UserWarning, LookupError) as e: │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/nf_core/components/update.py: │
│ 196 in update │
│ │
│ 193 │ │ │ │ continue │
│ 194 │ │ │ │
│ 195 │ │ │ if patch_relpath is not None: │
│ ❱ 196 │ │ │ │ patch_successful = self.try_apply_patch( │
│ 197 │ │ │ │ │ component, │
│ 198 │ │ │ │ │ modules_repo.repo_path, │
│ 199 │ │ │ │ │ patch_relpath, │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/nf_core/components/update.py: │
│ 788 in try_apply_patch │
│ │
│ 785 │ │ shutil.copytree(component_install_dir, temp_component_dir) │
│ 786 │ │ │
│ 787 │ │ try: │
│ ❱ 788 │ │ │ new_files = ModulesDiffer.try_apply_patch(component, repo_path, patch_path, │
│ 789 │ │ except LookupError: │
│ 790 │ │ │ # Patch failed. Save the patch file by moving to the install dir │
│ 791 │ │ │ shutil.move(patch_path, Path(component_install_dir, patch_path.relative_to(c │
│ │
│ /home/ec2-user/miniconda3/envs/nf-core/lib/python3.8/site-packages/nf_core/modules/modules_diffe │
│ r.py:450 in try_apply_patch │
│ │
│ 447 │ │ │ log.debug(f"Applying patch to {file}") │
│ 448 │ │ │ fn = Path(file).relative_to(module_relpath) │
│ 449 │ │ │ file_path = module_dir / fn │
│ ❱ 450 │ │ │ with open(file_path) as fh: │
│ 451 │ │ │ │ file_lines = fh.readlines() │
│ 452 │ │ │ patched_new_lines = ModulesDiffer.try_apply_single_patch(file_lines, patch, │
│ 453 │ │ │ new_files[str(fn)] = patched_new_lines │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpyqidsy9u/multiqc/nextflow.config'
System information
Nextflow version: 23.10.1.5891
Hardware: AWS EC2 t2.2xlarge
Executor: local
OS: Amazon Linux
Version of nf-core/tools: 2.12.1
Python version: 3.8.18
mirpedrol
commented
8 months ago
Description of the bug
Hi everyone!
I am unable to update a module with
nf-core modules update, even if the module has been patched withnf-core modules patchif the change I introduce is a new file in the folder, such as a nextflow.configIt would be nice if I could update the modules without reinstalling them when I add files.
Command used and terminal output
System information
Nextflow version: 23.10.1.5891 Hardware: AWS EC2 t2.2xlarge Executor: local OS: Amazon Linux Version of nf-core/tools: 2.12.1 Python version: 3.8.18