Comments (5)
mashehu
commented on September 2, 2024
what pipeline name did you try?
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mirpedrol
commented on September 2, 2024
Hi @adamrtalbot, hyphens are allowed in custom pipelines, how did you create your pipeline? I tested this behaviour and lining passes for me.
I opened #3094 to also allow numbers, for instance myorg-this-isap1pe_ did work when I tested that PR.
from tools.
adamrtalbot
commented on September 2, 2024
what pipeline name did you try?
wgs-pipeline
Still seeing the error with 930ece5
adamtalbot@vm-adamtalbot:~/wgs-pipeline$ nf-core --verbose pipelines lint
,--./,-.
___ __ __ __ ___ /,-._.--~\
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/tools version 2.14.2.dev0 - https://nf-co.re
DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/adamtalbot/wgs-pipeline, stdin=<valid stream>, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Using config file: .nf-core.yml utils.py:1060
DEBUG Got '.' as path utils.py:244
DEBUG Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json utils.py:278
DEBUG Popen(['git', 'version'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Using config file: /home/adamtalbot/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1060
DEBUG Using config file: .nf-core.yml utils.py:1060
DEBUG The following files were modified by prettier: lint_utils.py:88
modules.json
DEBUG Got '.' as path utils.py:244
DEBUG Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json utils.py:278
DEBUG Registry set to quay.io __init__.py:141
DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/adamtalbot/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1253
DEBUG Using config file: /home/adamtalbot/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1060
DEBUG Using config file: .nf-core.yml utils.py:1060
DEBUG The following files were modified by prettier: lint_utils.py:88
modules.json
DEBUG Got '.' as path utils.py:244
DEBUG Found a config cache, loading: /home/adamtalbot/.nextflow/nf-core/wf-config-cache-ba141f72800c1acee446fad4d.json utils.py:278
DEBUG Registry set to quay.io __init__.py:141
DEBUG Using config file: .nf-core.yml utils.py:1060
DEBUG Using config file: .nf-core.yml utils.py:1060
INFO Testing pipeline: . __init__.py:164
DEBUG Running lint test: files_exist __init__.py:227
DEBUG Found plugins in nextflow.config with value nf-validation files_exist.py:252
DEBUG Running lint test: nextflow_config __init__.py:227
DEBUG JSON file loaded: nextflow_schema.json schema.py:119
DEBUG Running lint test: files_unchanged __init__.py:227
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/adamtalbot/.local/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 │
│ │
│ /home/adamtalbot/.local/lib/python3.10/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( │
│ │
│ /home/adamtalbot/.local/lib/python3.10/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): │
│ │
│ /home/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/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! │
│ │
│ /home/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/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/adamtalbot/.local/lib/python3.10/site-packages/nf_core/__main__.py:348 in │
│ command_pipelines_lint │
│ │
│ 345 │ """ │
│ 346 │ Check pipeline code against nf-core guidelines. │
│ 347 │ """ │
│ ❱ 348 │ pipelines_lint(ctx, dir, release, fix, key, show_passed, fail_ignored, fail_warned, │
│ 349 │
│ 350 │
│ 351 # nf-core pipelines download │
│ │
│ /home/adamtalbot/.local/lib/python3.10/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 │ │ │ dir, │
│ 135 │ │ │ release, │
│ 136 │ │ │ fix, │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:603 in │
│ run_linting │
│ │
│ 600 │ │
│ 601 │ # Run the pipeline linting tests │
│ 602 │ try: │
│ ❱ 603 │ │ lint_obj._lint_pipeline() │
│ 604 │ except AssertionError as e: │
│ 605 │ │ log.critical(f"Critical error: {e}") │
│ 606 │ │ log.info("Stopping tests...") │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/__init__.py:228 in │
│ _lint_pipeline │
│ │
│ 225 │ │ │ │ │ continue │
│ 226 │ │ │ │ self.progress_bar.update(lint_progress, advance=1, test_name=test_name) │
│ 227 │ │ │ │ log.debug(f"Running lint test: {test_name}") │
│ ❱ 228 │ │ │ │ test_results = getattr(self, test_name)() │
│ 229 │ │ │ │ for test in test_results.get("passed", []): │
│ 230 │ │ │ │ │ self.passed.append((test_name, test)) │
│ 231 │ │ │ │ for test in test_results.get("ignored", []): │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/lint/files_unchanged.py:1 │
│ 30 in files_unchanged │
│ │
│ 127 │ │ yaml.dump(template_yaml, fh, default_flow_style=False) │
│ 128 │ │
│ 129 │ test_pipeline_dir = os.path.join(tmp_dir, f"{prefix}-{short_name}") │
│ ❱ 130 │ create_obj = nf_core.pipelines.create.create.PipelineCreate( │
│ 131 │ │ None, None, None, no_git=True, outdir=test_pipeline_dir, template_config=templat │
│ 132 │ ) │
│ 133 │ create_obj.init_pipeline() │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:74 in │
│ __init__ │
│ │
│ 71 │ │ │ template_config and (isinstance(template_config, str) or isinstance(template │
│ 72 │ │ ): │
│ 73 │ │ │ # Obtain a CreateConfig object from the template yaml file │
│ ❱ 74 │ │ │ self.config = self.check_template_yaml_info(template_config, name, descripti │
│ 75 │ │ │ self.update_config(organisation, version, force, outdir) │
│ 76 │ │ else: │
│ 77 │ │ │ raise UserWarning("The template configuration was not provided.") │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/create.py:145 in │
│ check_template_yaml_info │
│ │
│ 142 │ │ │ try: │
│ 143 │ │ │ │ with open(template_yaml) as f: │
│ 144 │ │ │ │ │ template_yaml = yaml.safe_load(f) │
│ ❱ 145 │ │ │ │ │ config = CreateConfig(**template_yaml) │
│ 146 │ │ │ except FileNotFoundError: │
│ 147 │ │ │ │ raise UserWarning(f"Template YAML file '{template_yaml}' not found.") │
│ 148 │
│ │
│ /home/adamtalbot/.local/lib/python3.10/site-packages/nf_core/pipelines/create/utils.py:53 in │
│ __init__ │
│ │
│ 50 │ │
│ 51 │ def __init__(self, /, **data: Any) -> None: │
│ 52 │ │ """Custom init method to allow using a context on the model initialization.""" │
│ ❱ 53 │ │ self.__pydantic_validator__.validate_python( │
│ 54 │ │ │ data, │
│ 55 │ │ │ self_instance=self, │
│ 56 │ │ │ context=_init_context_var.get(), │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ValidationError: 1 validation error for CreateConfig
name
Value error, Must not contain special characters. Only '-' or '_' are allowed. [type=value_error, input_value='wgs-pipeline', input_type=str]
For further information visit https://errors.pydantic.dev/2.8/v/value_error
from tools.
adamrtalbot
commented on September 2, 2024
Hmm might not be hyphens, let me try something.
from tools.
adamrtalbot
commented on September 2, 2024
Blegh, my bad. Solved it.
from tools.
Related Issues (20)
- nf-core create fails on 2.14.2.dev0 HOT 1
- No nf-core modules found HOT 8
- lint fails missing variables that are present HOT 6
- Fail to send the completion email
- Move --migrate-pytest command to `module test` command group HOT 2
- Add process_high_memory to create/lint list HOT 1
- Manual include or exclude specific files in template
- `xx` is present as an output in meta.yml but not in main.nf HOT 1
- Test pipelines with Singularity & Conda
- Print test directory path in output from `nf-core test`
- modules linting: Check that version.yml has version of all items in `environment.yml`
- `nf-core sync` does not respect existing template config on dev branch
- MultiQC results not cacheable
- nf-core/tools download error HOT 5
- Lint for test data paths and produce a warning/error if the config map is used?
- Add `-w`, `--fail-warned` option to `nf-core schema lint`
- Move igenomes config into pipeline code HOT 2
- Remove try-catch blocks around institutional configs HOT 14
- Add a linting test for the metro map
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