From 7619d9f470c07c05426b2c4c77232fe12aa29624 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 30 Jun 2026 13:01:17 +0000 Subject: [PATCH] [automated] Update nf-core/tools API docs for dev --- package-lock.json | 21 ---- .../api_reference/dev/api/nf_core_yml.md | 8 +- .../dev/api/pipelines/bump_version.md | 16 +-- .../api_reference/dev/api/pipelines/create.md | 18 ++-- .../dev/api/pipelines/download.md | 2 +- .../api_reference/dev/api/pipelines/index.md | 20 ++-- .../api_reference/dev/api/pipelines/launch.md | 16 +-- .../api_reference/dev/api/pipelines/lint.md | 10 +- .../dev/api/pipelines/lint_utils.md | 26 ++--- .../api_reference/dev/api/pipelines/list.md | 12 +-- .../dev/api/pipelines/params-file.md | 20 ++-- .../api_reference/dev/api/pipelines/schema.md | 6 +- .../api_reference/dev/api/pipelines/sync.md | 18 ++-- .../api_reference/dev/api/pipelines/utils.md | 2 +- .../content/api_reference/dev/api/utils.md | 100 +++++++++--------- .../dev/module_lint_tests/environment_yml.md | 2 +- .../dev/module_lint_tests/main_nf.md | 11 +- .../dev/module_lint_tests/meta_yml.md | 2 +- .../dev/module_lint_tests/module_changes.md | 2 +- .../module_lint_tests/module_deprecations.md | 2 +- .../dev/module_lint_tests/module_patch.md | 2 +- .../dev/module_lint_tests/module_tests.md | 2 +- .../dev/module_lint_tests/module_todos.md | 2 +- .../dev/module_lint_tests/module_version.md | 2 +- .../actions_awsfulltest.md | 2 +- .../pipeline_lint_tests/actions_awstest.md | 2 +- .../dev/pipeline_lint_tests/actions_ci.md | 2 +- .../pipeline_lint_tests/actions_nf_test.md | 2 +- .../actions_schema_validation.md | 2 +- .../dev/pipeline_lint_tests/base_config.md | 2 +- .../pipeline_lint_tests/container_configs.md | 2 +- .../dev/pipeline_lint_tests/files_exist.md | 6 +- .../pipeline_lint_tests/files_unchanged.md | 2 +- .../pipeline_lint_tests/included_configs.md | 4 +- .../local_component_structure.md | 2 +- .../dev/pipeline_lint_tests/merge_markers.md | 2 +- .../dev/pipeline_lint_tests/modules_config.md | 2 +- .../dev/pipeline_lint_tests/modules_json.md | 2 +- .../pipeline_lint_tests/modules_structure.md | 2 +- .../dev/pipeline_lint_tests/multiqc_config.md | 8 +- .../pipeline_lint_tests/nextflow_config.md | 4 +- .../pipeline_lint_tests/nf_test_content.md | 2 +- .../dev/pipeline_lint_tests/nfcore_yml.md | 2 +- .../pipeline_if_empty_null.md | 2 +- .../pipeline_name_conventions.md | 2 +- .../dev/pipeline_lint_tests/pipeline_todos.md | 2 +- .../pipeline_lint_tests/plugin_includes.md | 2 +- .../rocrate_readme_sync.md | 2 +- .../pipeline_lint_tests/schema_description.md | 2 +- .../dev/pipeline_lint_tests/schema_lint.md | 2 +- .../dev/pipeline_lint_tests/schema_params.md | 2 +- .../dev/pipeline_lint_tests/system_exit.md | 2 +- .../pipeline_lint_tests/template_strings.md | 2 +- .../version_consistency.md | 2 +- .../dev/subworkflow_lint_tests/main_nf.md | 2 +- .../dev/subworkflow_lint_tests/meta_yml.md | 2 +- .../subworkflow_changes.md | 2 +- .../subworkflow_if_empty_null.md | 2 +- .../subworkflow_tests.md | 2 +- .../subworkflow_todos.md | 2 +- .../subworkflow_version.md | 2 +- 61 files changed, 199 insertions(+), 211 deletions(-) diff --git a/package-lock.json b/package-lock.json index 22e0c42e64..80f2f41a18 100644 --- a/package-lock.json +++ b/package-lock.json @@ -17329,7 +17329,6 @@ "integrity": "sha512-B5j0rYMlinhhOo9tjQebMVVn0TfyXAF+wB3b2ggZUuJ/is/Y+7+JGjirAMxHZ9Z3hIP98NPfamlAkBHa1lAaXQ==", "license": "MIT", "optional": true, - "peer": true, "dependencies": { "chokidar": "^5.0.0", "immutable": "^5.1.5", @@ -17399,7 +17398,6 @@ ], "license": "MIT", "optional": true, - "peer": true, "dependencies": { "sass": "1.100.0" } @@ -17416,7 +17414,6 @@ "os": [ "android" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17433,7 +17430,6 @@ "os": [ "android" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17450,7 +17446,6 @@ "os": [ "android" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17467,7 +17462,6 @@ "os": [ "android" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17484,7 +17478,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17501,7 +17494,6 @@ "os": [ "darwin" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17518,7 +17510,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17535,7 +17526,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17552,7 +17542,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17569,7 +17558,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17586,7 +17574,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17603,7 +17590,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17620,7 +17606,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17637,7 +17622,6 @@ "os": [ "linux" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17654,7 +17638,6 @@ "!linux", "!win32" ], - "peer": true, "dependencies": { "sass": "1.100.0" } @@ -17671,7 +17654,6 @@ "os": [ "win32" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17688,7 +17670,6 @@ "os": [ "win32" ], - "peer": true, "engines": { "node": ">=14.0.0" } @@ -17709,7 +17690,6 @@ "integrity": "sha512-TQMmc3w+5AxjpL8iIiwebF73dRDF4fBIieAqGn9RGCWaEVwQ6Fb2cGe31Yns0RRIzii5goJ1Y7xbMwo1TxMplw==", "license": "MIT", "optional": true, - "peer": true, "dependencies": { "readdirp": "^5.0.0" }, @@ -17726,7 +17706,6 @@ "integrity": "sha512-9u/XQ1pvrQtYyMpZe7DXKv2p5CNvyVwzUB6uhLAnQwHMSgKMBR62lc7AHljaeteeHXn11XTAaLLUVZYVZyuRBQ==", "license": "MIT", "optional": true, - "peer": true, "engines": { "node": ">= 20.19.0" }, diff --git a/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md b/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md index 9496b6bc27..466c193a44 100644 --- a/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md +++ b/sites/docs/src/content/api_reference/dev/api/nf_core_yml.md @@ -44,7 +44,7 @@ Bases: `BaseModel` #### _`field{:python}`_`bump_version{:python}`_: dict\[str, bool] | None_`{:python}`_= None_ -Disable bumping of the version for a module/subworkflow (when repository_type is modules). See for more information. +Disable bumping of the version for a module/subworkflow (when repository\_type is modules). See for more information. #### _`field{:python}`_`container_registry{:python}`_: list\[str] | None_`{:python}`_= None_`{:python}`_(alias 'container-registry')_ @@ -60,7 +60,7 @@ Version of nf-core/tools used to create/update the pipeline #### _`field{:python}`_`org_path{:python}`_: str | None_`{:python}`_= None_ -Path to the organisation’s modules repository (used for modules repo_type only) +Path to the organisation’s modules repository (used for modules repo\_type only) #### _`field{:python}`_`repository_type{:python}`_: Literal\['pipeline', 'modules'] | None_`{:python}`_= None_ @@ -72,7 +72,7 @@ Pipeline template configuration #### _`field{:python}`_`update{:python}`_: dict\[str, str | bool | dict\[str, str | dict\[str, str | bool]]] | None_`{:python}`_= None_ -Disable updating specific modules/subworkflows (when repository_type is pipeline). See for more information. +Disable updating specific modules/subworkflows (when repository\_type is pipeline). See for more information. ### `lint``block ({:python}``NFCoreYamlLintConfig``){:python}` @@ -254,7 +254,7 @@ Check that every parameter in the schema has a description. #### _`field{:python}`_`schema_lint{:python}`_: bool | None_`{:python}`_= None_ -Lint nextflow_schema.json file +Lint nextflow\_schema.json file #### _`field{:python}`_`schema_params{:python}`_: bool | None_`{:python}`_= None_ diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/bump_version.md b/sites/docs/src/content/api_reference/dev/api/pipelines/bump_version.md index 88a1f8243e..fc6cbc9556 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/bump_version.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/bump_version.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.bump_version +# nf\_core.pipelines.bump\_version Bumps the version number in all appropriate files for a nf-core pipeline. @@ -8,18 +8,18 @@ a nf-core pipeline. Bumps the required Nextflow version number of a pipeline. - **Parameters:** - - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information + - **pipeline\_obj** ([_nf\_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information about the pipeline contents and build files. - - **new_version** (_str_) – The new version tag for the required Nextflow version. + - **new\_version** (_str_) – The new version tag for the required Nextflow version. ### `nf_core.pipelines.bump_version.bump_pipeline_version(pipeline_obj:{:python}`[`Pipeline{:python}`](../utils#nf_core.utils.Pipeline)`, new_version: str) → None{:python}` Bumps a pipeline version number. - **Parameters:** - - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information + - **pipeline\_obj** ([_nf\_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information about the pipeline contents and build files. - - **new_version** (_str_) – The new version tag for the pipeline. Semantic versioning only. + - **new\_version** (_str_) – The new version tag for the pipeline. Semantic versioning only. ### `nf_core.pipelines.bump_version.handle_error(message: str, required: bool){:python}` @@ -31,12 +31,12 @@ Updates a file with a new version number. - **Parameters:** - **filename** (_str_) – The name of the file to update. - - **pipeline_obj** ([_nf_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information + - **pipeline\_obj** ([_nf\_core.utils.Pipeline_](../utils#nf_core.utils.Pipeline)) – A Pipeline object that holds information about the pipeline contents. - **patterns** (_List_ \*\[\*_Tuple_ \*\[\*_str_ _,_ _str_ _]_ _]_) – A list of tuples containing the regex patterns to match and the replacement strings. - **required** (_bool_ _,_ _optional_) – Whether the file is required to exist. Defaults to True. - - **yaml_key** (_List_ \*\[\*_str_ _]_ _|_ _None_ _,_ _optional_) – The YAML key to update. Defaults to None. + - **yaml\_key** (_List_ \*\[\*_str_ _]_ _|_ _None_ _,_ _optional_) – The YAML key to update. Defaults to None. ### `nf_core.pipelines.bump_version.update_text_file(fn: Path, patterns: list[tuple[str, str]], required: bool){:python}` @@ -56,5 +56,5 @@ Updates a YAML file with a new version number. - **fn** (_Path_) – The name of the file to update. - **patterns** (_List_ \*\[\*_Tuple_ \*\[\*_str_ _,_ _str_ _]_ _]_) – A list of tuples containing the regex patterns to match and the replacement strings. - - **yaml_key** (_List_ \*\[\*_str_ _]_) – The YAML key to update. + - **yaml\_key** (_List_ \*\[\*_str_ _]_) – The YAML key to update. - **required** (_bool_) – Whether the file is required to exist. diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/create.md b/sites/docs/src/content/api_reference/dev/api/pipelines/create.md index 506e4995b6..dc96e1f52d 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/create.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/create.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.create +# nf\_core.pipelines.create A Textual app to create a pipeline. @@ -8,7 +8,7 @@ Bases: `App`\[`CreateConfig`] A Textual app to manage stopwatches. -#### `BINDINGS{:python}`_= \[('d', 'toggle_dark', 'Toggle dark mode'), ('q', 'quit', 'Quit'), ('a', 'toggle_all', 'Toggle all')]_ +#### `BINDINGS{:python}`_= \[('d', 'toggle\_dark', 'Toggle dark mode'), ('q', 'quit', 'Quit'), ('a', 'toggle\_all', 'Toggle all')]_ The default key bindings. @@ -22,7 +22,7 @@ File paths to load CSS from. #### `NFCORE_PIPELINE{:python}`_= True_ -#### `SCREENS{:python}`_= {'basic_details': \, 'choose_type': \, 'final_details': \, 'github_exit': \, 'github_repo': \, 'github_repo_question': \, 'logging': \, 'type_custom': \, 'type_nfcore': \, 'welcome': \}_ +#### `SCREENS{:python}`_= {'basic\_details': \, 'choose\_type': \, 'final\_details': \, 'github\_exit': \, 'github\_repo': \, 'github\_repo\_question': \, 'logging': \, 'type\_custom': \, 'type\_nfcore': \, 'welcome': \}_ Screens associated with the app for the lifetime of the app. @@ -30,10 +30,10 @@ Screens associated with the app for the lifetime of the app. A class variable to set the default sub-title for the application. -To update the sub-title while the app is running, you can set the \[sub_title]\[textual.app.App.sub_title] attribute. -See also \[the Screen.SUB_TITLE attribute]\[textual.screen.Screen.SUB_TITLE]. +To update the sub-title while the app is running, you can set the \[sub\_title]\[textual.app.App.sub\_title] attribute. +See also \[the Screen.SUB\_TITLE attribute]\[textual.screen.Screen.SUB\_TITLE]. -#### `TEMPLATE_CONFIG{:python}`_= CreateConfig(org=None, name=None, description=None, author=None, version=None, force=True, outdir=None, skip_features=None, is_nfcore=None)_ +#### `TEMPLATE_CONFIG{:python}`_= CreateConfig(org=None, name=None, description=None, author=None, version=None, force=True, outdir=None, skip\_features=None, is\_nfcore=None)_ #### `TITLE{:python}`_= 'nf-core pipelines create'_ @@ -56,9 +56,9 @@ See also \[the Screen.TITLE attribute]\[textual.screen.Screen.TITLE]. #### `_inherit_css{:python}`_= True_ -#### `_merged_bindings{:python}`_= BindingsMap({'ctrl+q': \[Binding(key='ctrl+q', action='quit', description='Quit', show=False, key_display=None, priority=True, tooltip='Quit the app and return to the command prompt.', id=None, system=False, group=None)], 'ctrl+c': \[Binding(key='ctrl+c', action='help_quit', description='', show=False, key_display=None, priority=False, tooltip='', id=None, system=True, group=None)], 'd': \[Binding(key='d', action='toggle_dark', description='Toggle dark mode', show=True, key_display=None, priority=False, tooltip='', id=None, system=False, group=None)], 'q': \[Binding(key='q', action='quit', description='Quit', show=True, key_display=None, priority=False, tooltip='', id=None, system=False, group=None)], 'a': \[Binding(key='a', action='toggle_all', description='Toggle all', show=True, key_display=None, priority=False, tooltip='', id=None, system=False, group=None)]})_ +#### `_merged_bindings{:python}`_= BindingsMap({'ctrl+q': \[Binding(key='ctrl+q', action='quit', description='Quit', show=False, key\_display=None, priority=True, tooltip='Quit the app and return to the command prompt.', id=None, system=False, group=None)], 'ctrl+c': \[Binding(key='ctrl+c', action='help\_quit', description='', show=False, key\_display=None, priority=False, tooltip='', id=None, system=True, group=None)], 'd': \[Binding(key='d', action='toggle\_dark', description='Toggle dark mode', show=True, key\_display=None, priority=False, tooltip='', id=None, system=False, group=None)], 'q': \[Binding(key='q', action='quit', description='Quit', show=True, key\_display=None, priority=False, tooltip='', id=None, system=False, group=None)], 'a': \[Binding(key='a', action='toggle\_all', description='Toggle all', show=True, key\_display=None, priority=False, tooltip='', id=None, system=False, group=None)]})_ -#### `_reactives{:python}`_= {'ansi_color': Reactive(False, name='ansi_color'), 'ansi_theme_dark': Reactive(\, name='ansi_theme_dark'), 'ansi_theme_light': Reactive(\, name='ansi_theme_light'), 'app_focus': Reactive(True, compute=False, name='app_focus'), 'sub_title': Reactive('', compute=False, name='sub_title'), 'theme': Reactive('textual-dark', name='theme'), 'title': Reactive('', compute=False, name='title')}_ +#### `_reactives{:python}`_= {'ansi\_color': Reactive(False, name='ansi\_color'), 'ansi\_theme\_dark': Reactive(\, name='ansi\_theme\_dark'), 'ansi\_theme\_light': Reactive(\, name='ansi\_theme\_light'), 'app\_focus': Reactive(True, compute=False, name='app\_focus'), 'sub\_title': Reactive('', compute=False, name='sub\_title'), 'theme': Reactive('textual-dark', name='theme'), 'title': Reactive('', compute=False, name='title')}_ #### `action_toggle_all() → None{:python}` @@ -74,4 +74,4 @@ Handle all button pressed events. #### `on_mount() → None{:python}` -#### `template_features_yml{:python}`_= {'code_quality': {'features': {'code_linters': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.', 'help_text': 'Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.\nLinters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.\nThe available code linters are:\n\n- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run \`pre-commit install\` to install it in your local repository.\n- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).\n', 'linting': {'files_exist': \['.prettierignore', '.prettierrc.yml']}, 'nfcore_pipelines': False, 'short_description': 'Use code linters', 'skippable_paths': \['.pre-commit-config.yaml', '.prettierignore', '.prettierrc.yml', '.github/workflows/fix-linting.yml']}}, 'name': 'Code Quality'}, 'components_modules': {'features': {'fastqc': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files.', 'help_text': 'FastQC is a tool which provides quality control checks on raw sequencing data.\nThe pipeline will include the FastQC module.\n', 'nfcore_pipelines': True, 'short_description': 'Use fastqc', 'skippable_paths': \['modules/nf-core/fastqc/']}, 'igenomes': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will be configured to use a copy of the most common reference genome files from iGenomes', 'help_text': 'Nf-core pipelines are configured to use a copy of the most common reference genome files.\n\nBy selecting this option, your pipeline will include a configuration file specifying the paths to these files.\n\nThe required code to use these files will also be included in the template.\nWhen the pipeline user provides an appropriate genome key,\nthe pipeline will automatically download the required reference files.\n\nFor more information about reference genomes in nf-core pipelines,\nsee the [nf-core docs](https://nf-co.re/docs/running/reference-genomes).\n', 'linting': {'files_exist': \['conf/igenomes.config', 'conf/igenomes_ignored.config']}, 'nfcore_pipelines': True, 'short_description': 'Use reference genomes', 'skippable_paths': \['conf/igenomes.config', 'conf/igenomes_ignored.config']}, 'modules': {'custom_pipelines': True, 'default': True, 'description': 'Include all required files to use nf-core modules and subworkflows', 'help_text': 'It is \*recommended\* to use this feature if you want to use modules and subworkflows in your pipeline.\nThis will add all required files to use nf-core components or any compatible components from private repos by using \`nf-core modules\` and \`nf-core subworkflows\` commands.\n', 'linting': {'base_config': False, 'files_exist': \['conf/base.config', 'conf/modules.config', 'modules.json'], 'files_unchanged': \['.prettierignore'], 'modules_config': False, 'modules_json': False, 'nfcore_components': False}, 'nfcore_pipelines': False, 'short_description': 'Use nf-core components', 'skippable_paths': \['conf/base.config', 'conf/modules.config', 'modules.json', 'modules', 'subworkflows']}, 'multiqc': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include the MultiQC module which generates an HTML report for quality control.', 'help_text': 'MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.\n\nThe pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.\n', 'linting': {'files_exist': \['assets/multiqc_config.yml'], 'files_unchanged': \['assets/sendmail_template.txt'], 'multiqc_config': False}, 'nfcore_pipelines': True, 'short_description': 'Use multiqc', 'skippable_paths': \['assets/multiqc_config.yml', 'assets/methods_description_template.yml', 'modules/nf-core/multiqc/']}, 'nf_schema': {'custom_pipelines': True, 'default': True, 'description': 'Use the nf-schema Nextflow plugin for this pipeline.', 'help_text': '[nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.\nIt also provides helper functionality to create help messages, get a summary\nof changed parameters and validate and convert a samplesheet to a channel.\n', 'linting': {'files_exist': \['nextflow_schema.json'], 'nextflow_config': False, 'schema_description': False, 'schema_lint': False, 'schema_params': False}, 'nfcore_pipelines': True, 'short_description': 'Use nf-schema', 'skippable_paths': \['subworkflows/nf-core/utils_nfschema_plugin', 'nextflow_schema.json', 'assets/schema_input.json', 'assets/samplesheet.csv']}}, 'name': 'Components & Modules'}, 'configurations': {'features': {'gpu': {'custom_pipelines': True, 'default': False, 'description': 'Add GPU support to the pipeline', 'help_text': 'This will add GPU support to the pipeline. It will add a \`use_gpu\` parameter to the pipeline.\nThe pipeline will be able to run on GPU-enabled compute environments.\n', 'nfcore_pipelines': True, 'short_description': 'Use GPU', 'skippable_paths': False}, 'is_nfcore': {'custom_pipelines': False, 'default': True, 'description': '', 'help_text': '', 'linting': {'files_exist': \['CODE_OF_CONDUCT.md', 'assets/nf-core-{{short\_name}}\_logo_light.png', 'docs/images/nf-core-{{short\_name}}\_logo_light.png', 'docs/images/nf-core-{{short\_name}}\_logo_dark.png', '.github/ISSUE_TEMPLATE/config.yml', '.github/workflows/awstest.yml', '.github/workflows/awsfulltest.yml'], 'files_unchanged': \['CODE_OF_CONDUCT.md', 'assets/nf-core-{{short\_name}}\_logo_light.png', 'docs/images/nf-core-{{short\_name}}\_logo_light.png', 'docs/images/nf-core-{{short\_name}}\_logo_dark.png', '.github/ISSUE_TEMPLATE/bug_report.yml', '.github/PULL_REQUEST_TEMPLATE.md', 'assets/email_template.txt', 'docs/README.md'], 'multiqc_config': \['report_comment'], 'nextflow_config': \['manifest.name', 'manifest.homePage']}, 'nfcore_pipelines': False, 'short_description': "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools.", 'skippable_paths': \['.github/ISSUE_TEMPLATE/config', 'CODE_OF_CONDUCT.md', '.github/workflows/awsfulltest.yml', '.github/workflows/awstest.yml', '.github/workflows/release-announcements.yml']}, 'nf_core_configs': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include configuration profiles containing custom parameters required to run nf-core pipelines at different institutions', 'help_text': 'Nf-core has a repository with a collection of configuration profiles.\n\nThose config files define a set of parameters which are specific to compute environments at different Institutions.\nThey can be used within all nf-core pipelines.\nIf you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation.\n\nFor more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)\n', 'linting': {'files_exist': \['conf/igenomes.config'], 'included_configs': False, 'nextflow_config': \['process.cpus', 'process.memory', 'process.time', 'custom_config', 'params.custom_config_version', 'params.custom_config_base']}, 'nfcore_pipelines': False, 'short_description': 'Add configuration files', 'skippable_paths': False}, 'seqera_platform': {'custom_pipelines': True, 'default': True, 'description': 'Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform', 'help_text': 'When launching a pipeline with the Seqera Platform, a \`tower.yml\` file can be used to add configuration options.\n\nIn the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform.\nYou can extend this file adding any other desired configuration.\n', 'nfcore_pipelines': False, 'short_description': 'Add Seqera Platform output', 'skippable_paths': \['tower.yml']}}, 'name': 'Configurations'}, 'continuous_integration_testing': {'features': {'ci': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include several GitHub actions for Continuous Integration (CI) testing', 'help_text': 'Nf-core provides a set of Continuous Integration (CI) tests for Github.\nWhen you open a pull request (PR) on your pipeline repository, these tests will run automatically.\n\nThere are different types of tests:\n\* Linting tests check that your code is formatted correctly and that it adheres to nf-core standards\n For code linting they will use [prettier](https://prettier.io/).\n\* Pipeline tests run your pipeline on a small dataset to check that it works\n These tests are run with a small test dataset on GitHub and a larger test dataset on AWS\n\* Marking old issues as stale\n', 'linting': {'files_exist': \['.github/workflows/branch.yml', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', '.github/workflows/linting_comment.yml', '.github/workflows/linting.yml']}, 'nfcore_pipelines': False, 'short_description': 'Add Github CI tests', 'skippable_paths': \['.github/workflows/']}, 'nf-test': {'custom_pipelines': True, 'default': True, 'description': 'Add pipeline testing using nf-test', 'help_text': "This will add pipeline testing with [nf-test](https://www.nf-test.com/).\n\nWill add and \`nf-test.config\` file setting up the appropriate configuration to test your pipeline.\nOn top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests.\n\nIf you skip this feature, you will still be able to test your pipeline with a \`test\` profile by running the pipeline.\nBut you won't have the automated CI testing.\nYou can add CI by yourself.\n", 'linting': {'files_exist': \['.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', 'nf-test.config', 'tests/default.nf.test'], 'nf_test_content': False}, 'nfcore_pipelines': False, 'short_description': 'Add pipeline testing', 'skippable_paths': \['.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', 'nf-test.config', 'tests/default.nf.test', 'tests/.nftignore', 'tests/nextflow.config']}, 'test_config': {'custom_pipelines': True, 'default': True, 'description': 'Add two default testing profiles', 'help_text': 'This will add two default testing profiles to run the pipeline with different inputs.\nYou can customise them and add other test profiles.\n\nThese profiles can be used to run the pipeline with a minimal testing dataset with \`nextflow run \ -profile test\`.\n\nThe pipeline will include two profiles: \`test\` and \`test_full\`.\nIn nf-core, we typically use the \`test\` profile to run the pipeline with a minimal dataset and the \`test_full\` to run the pipeline with a larger dataset that simulates a real-world scenario.\n', 'linting': {'files_exist': \['conf/test.config', 'conf/test_full.config', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml'], 'files_unchanged': \['.github/PULL_REQUEST_TEMPLATE.md'], 'nextflow_config': False}, 'nfcore_pipelines': False, 'short_description': 'Add testing profiles', 'skippable_paths': \['conf/test.config', 'conf/test_full.config', '.github/workflows/awsfulltest.yml', '.github/workflows/awstest.yml', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml']}}, 'name': 'Continuous Integration & Testing'}, 'development_environments': {'features': {'codespaces': {'custom_pipelines': True, 'default': True, 'description': 'The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.', 'help_text': 'The pipeline will include a devcontainer configuration.\nThe devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.\n\nGithub Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.\n', 'linting': {'files_unchanged': \['docs/CONTRIBUTING.md']}, 'nfcore_pipelines': False, 'short_description': 'Include GitHub Codespaces', 'skippable_paths': \['.devcontainer/devcontainer.json', '.devcontainer/setup.sh']}, 'vscode': {'custom_pipelines': True, 'default': True, 'description': 'Add a VSCode configuration to render website admonitions', 'help_text': 'This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website.\n\nAdds the \`.vscode\` directory to the pipelinerepository.\n', 'nfcore_pipelines': False, 'short_description': 'Render website admonitions in VSCode', 'skippable_paths': \['.vscode']}}, 'name': 'Development Environments'}, 'documentation_metadata': {'features': {'citations': {'custom_pipelines': True, 'default': True, 'description': 'Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).', 'help_text': 'If adding citations, the pipeline template will contain a \`CITATIONS.md\` file to add the citations of all tools used in the pipeline.\n\nAdditionally, it will include a YAML file (\`assets/methods_description_template.yml\`) to add a Materials & Methods section describing the tools used in the pieline,\nand the logics to add this section to the output MultiQC report (if the report is generated).\n', 'linting': {'files_exist': \['CITATIONS.md']}, 'nfcore_pipelines': False, 'short_description': 'Include citations', 'skippable_paths': \['assets/methods_description_template.yml', 'CITATIONS.md']}, 'documentation': {'custom_pipelines': True, 'default': True, 'description': 'Add documentation to the pipeline', 'help_text': 'This will add documentation markdown files where you can describe your pipeline.\nIt includes:\n- docs/CONTRIBUTING.md: A contributing guide to help others contribute to your pipeline.\n- docs/README.md: A README file where you can describe the structure of your documentation.\n- docs/output.md: A file where you can explain the output generated by the pipeline\n- docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.\n\nThese files come with an exemplary documentation structure written.\n', 'linting': {'files_exist': \['docs/CONTRIBUTING.md', 'docs/output.md', 'docs/README.md', 'docs/usage.md']}, 'nfcore_pipelines': False, 'short_description': 'Add documentation', 'skippable_paths': \['docs']}, 'rocrate': {'custom_pipelines': True, 'default': True, 'description': 'Add a RO-Crate metadata file to describe the pipeline', 'help_text': 'RO-Crate is a metadata specification to describe research data and software.\nThis will add a \`ro-crate-metadata.json\` file to describe the pipeline.\n', 'linting': {'files_unchanged': \['.prettierignore'], 'files_warn': \['ro-crate-metadata.json']}, 'nfcore_pipelines': False, 'short_description': 'Add RO-Crate metadata', 'skippable_paths': \['ro-crate-metadata.json']}}, 'name': 'Documentation & metadata'}, 'notifications': {'features': {'email': {'custom_pipelines': True, 'default': True, 'description': 'Enable sending emails on pipeline completion.', 'help_text': 'Enable the option of sending an email which will include pipeline execution reports on pipeline completion.\n', 'linting': {'files_exist': \['assets/email_template.html', 'assets/sendmail_template.txt', 'assets/email_template.txt'], 'files_unchanged': \['.prettierignore']}, 'nfcore_pipelines': False, 'short_description': 'Enable email updates', 'skippable_paths': \['assets/email_template.html', 'assets/sendmail_template.txt', 'assets/email_template.txt']}}, 'name': 'Notifications'}, 'repository_setup': {'features': {'changelog': {'custom_pipelines': True, 'default': True, 'description': 'Add a CHANGELOG.md file.', 'help_text': 'Having a \`CHANGELOG.md\` file in the pipeline root directory is useful to track the changes added to each version.\n\nYou can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/\n', 'linting': {'files_exist': \['CHANGELOG.md']}, 'nfcore_pipelines': False, 'short_description': 'Add a changelog', 'skippable_paths': \['CHANGELOG.md']}, 'github': {'custom_pipelines': True, 'default': True, 'description': 'Create a GitHub repository for the pipeline.', 'help_text': 'This will create a GitHub repository for the pipeline.\n\nThe repository will include:\n- Continuous Integration (CI) tests\n- Issues and pull requests templates\n\nThe initialisation of a git repository is required to use the nf-core/tools.\nThis means that even if you unselect this option, your pipeline will still contain a \`.git\` directory and \`.gitignore\` file.\n', 'linting': {'files_exist': \['.github/ISSUE_TEMPLATE/bug_report.yml', '.github/ISSUE_TEMPLATE/feature_request.yml', '.github/PULL_REQUEST_TEMPLATE.md', '.github/.dockstore.yml', 'docs/CONTRIBUTING.md'], 'files_unchanged': \['.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/.dockstore.yml'], 'readme': \['nextflow_badge']}, 'nfcore_pipelines': False, 'short_description': 'Use a GitHub repository.', 'skippable_paths': \['.github', '.gitattributes']}, 'github_badges': {'custom_pipelines': True, 'default': True, 'description': 'The README.md file of the pipeline will include GitHub badges', 'help_text': 'The pipeline \`README.md\` will include badges for:\n\* AWS CI Tests\n\* Zenodo DOI\n\* Nextflow\n\* nf-core template version\n\* Conda\n\* Docker\n\* Singularity\n\* Launching on Nextflow Tower\n', 'linting': {'readme': \['nextflow_badge', 'nfcore_template_badge']}, 'nfcore_pipelines': False, 'short_description': 'Add Github badges', 'skippable_paths': False}, 'license': {'custom_pipelines': True, 'default': True, 'description': 'Add the MIT license file.', 'help_text': 'To protect the copyright of the pipeline, you can add a LICENSE file.\nThis option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT\n', 'linting': {'files_exist': \['LICENSE'], 'files_unchanged': \['LICENSE']}, 'nfcore_pipelines': False, 'short_description': 'Add a license File', 'skippable_paths': \['LICENSE']}}, 'name': 'Repository Setup'}}_ +#### `template_features_yml{:python}`_= {'code\_quality': {'features': {'code\_linters': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier.', 'help\_text': 'Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers.\nLinters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository.\nThe available code linters are:\n\n- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run \`pre-commit install\` to install it in your local repository.\n- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).\n', 'linting': {'files\_exist': \['.prettierignore', '.prettierrc.yml']}, 'nfcore\_pipelines': False, 'short\_description': 'Use code linters', 'skippable\_paths': \['.pre-commit-config.yaml', '.prettierignore', '.prettierrc.yml', '.github/workflows/fix-linting.yml']}}, 'name': 'Code Quality'}, 'components\_modules': {'features': {'fastqc': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files.', 'help\_text': 'FastQC is a tool which provides quality control checks on raw sequencing data.\nThe pipeline will include the FastQC module.\n', 'nfcore\_pipelines': True, 'short\_description': 'Use fastqc', 'skippable\_paths': \['modules/nf-core/fastqc/']}, 'igenomes': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will be configured to use a copy of the most common reference genome files from iGenomes', 'help\_text': 'Nf-core pipelines are configured to use a copy of the most common reference genome files.\n\nBy selecting this option, your pipeline will include a configuration file specifying the paths to these files.\n\nThe required code to use these files will also be included in the template.\nWhen the pipeline user provides an appropriate genome key,\nthe pipeline will automatically download the required reference files.\n\nFor more information about reference genomes in nf-core pipelines,\nsee the [nf-core docs](https://nf-co.re/docs/running/reference-genomes).\n', 'linting': {'files\_exist': \['conf/igenomes.config', 'conf/igenomes\_ignored.config']}, 'nfcore\_pipelines': True, 'short\_description': 'Use reference genomes', 'skippable\_paths': \['conf/igenomes.config', 'conf/igenomes\_ignored.config']}, 'modules': {'custom\_pipelines': True, 'default': True, 'description': 'Include all required files to use nf-core modules and subworkflows', 'help\_text': 'It is \*recommended\* to use this feature if you want to use modules and subworkflows in your pipeline.\nThis will add all required files to use nf-core components or any compatible components from private repos by using \`nf-core modules\` and \`nf-core subworkflows\` commands.\n', 'linting': {'base\_config': False, 'files\_exist': \['conf/base.config', 'conf/modules.config', 'modules.json'], 'files\_unchanged': \['.prettierignore'], 'modules\_config': False, 'modules\_json': False, 'nfcore\_components': False}, 'nfcore\_pipelines': False, 'short\_description': 'Use nf-core components', 'skippable\_paths': \['conf/base.config', 'conf/modules.config', 'modules.json', 'modules', 'subworkflows']}, 'multiqc': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include the MultiQC module which generates an HTML report for quality control.', 'help\_text': 'MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory.\n\nThe pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info.\n', 'linting': {'files\_exist': \['assets/multiqc\_config.yml'], 'files\_unchanged': \['assets/sendmail\_template.txt'], 'multiqc\_config': False}, 'nfcore\_pipelines': True, 'short\_description': 'Use multiqc', 'skippable\_paths': \['assets/multiqc\_config.yml', 'assets/methods\_description\_template.yml', 'modules/nf-core/multiqc/']}, 'nf\_schema': {'custom\_pipelines': True, 'default': True, 'description': 'Use the nf-schema Nextflow plugin for this pipeline.', 'help\_text': '[nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.\nIt also provides helper functionality to create help messages, get a summary\nof changed parameters and validate and convert a samplesheet to a channel.\n', 'linting': {'files\_exist': \['nextflow\_schema.json'], 'nextflow\_config': False, 'schema\_description': False, 'schema\_lint': False, 'schema\_params': False}, 'nfcore\_pipelines': True, 'short\_description': 'Use nf-schema', 'skippable\_paths': \['subworkflows/nf-core/utils\_nfschema\_plugin', 'nextflow\_schema.json', 'assets/schema\_input.json', 'assets/samplesheet.csv']}}, 'name': 'Components & Modules'}, 'configurations': {'features': {'gpu': {'custom\_pipelines': True, 'default': False, 'description': 'Add GPU support to the pipeline', 'help\_text': 'This will add GPU support to the pipeline. It will add a \`use\_gpu\` parameter to the pipeline.\nThe pipeline will be able to run on GPU-enabled compute environments.\n', 'nfcore\_pipelines': True, 'short\_description': 'Use GPU', 'skippable\_paths': False}, 'is\_nfcore': {'custom\_pipelines': False, 'default': True, 'description': '', 'help\_text': '', 'linting': {'files\_exist': \['CODE\_OF\_CONDUCT.md', 'assets/nf-core-{{short\_name}}\_logo\_light.png', 'docs/images/nf-core-{{short\_name}}\_logo\_light.png', 'docs/images/nf-core-{{short\_name}}\_logo\_dark.png', '.github/ISSUE\_TEMPLATE/config.yml', '.github/workflows/awstest.yml', '.github/workflows/awsfulltest.yml'], 'files\_unchanged': \['CODE\_OF\_CONDUCT.md', 'assets/nf-core-{{short\_name}}\_logo\_light.png', 'docs/images/nf-core-{{short\_name}}\_logo\_light.png', 'docs/images/nf-core-{{short\_name}}\_logo\_dark.png', '.github/ISSUE\_TEMPLATE/bug\_report.yml', '.github/PULL\_REQUEST\_TEMPLATE.md', 'assets/email\_template.txt', 'docs/README.md'], 'multiqc\_config': \['report\_comment'], 'nextflow\_config': \['manifest.name', 'manifest.homePage']}, 'nfcore\_pipelines': False, 'short\_description': "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools.", 'skippable\_paths': \['.github/ISSUE\_TEMPLATE/config', 'CODE\_OF\_CONDUCT.md', '.github/workflows/awsfulltest.yml', '.github/workflows/awstest.yml', '.github/workflows/release-announcements.yml']}, 'nf\_core\_configs': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include configuration profiles containing custom parameters required to run nf-core pipelines at different institutions', 'help\_text': 'Nf-core has a repository with a collection of configuration profiles.\n\nThose config files define a set of parameters which are specific to compute environments at different Institutions.\nThey can be used within all nf-core pipelines.\nIf you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation.\n\nFor more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs)\n', 'linting': {'files\_exist': \['conf/igenomes.config'], 'included\_configs': False, 'nextflow\_config': \['process.cpus', 'process.memory', 'process.time', 'custom\_config', 'params.custom\_config\_version', 'params.custom\_config\_base']}, 'nfcore\_pipelines': False, 'short\_description': 'Add configuration files', 'skippable\_paths': False}, 'seqera\_platform': {'custom\_pipelines': True, 'default': True, 'description': 'Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform', 'help\_text': 'When launching a pipeline with the Seqera Platform, a \`tower.yml\` file can be used to add configuration options.\n\nIn the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform.\nYou can extend this file adding any other desired configuration.\n', 'nfcore\_pipelines': False, 'short\_description': 'Add Seqera Platform output', 'skippable\_paths': \['tower.yml']}}, 'name': 'Configurations'}, 'continuous\_integration\_testing': {'features': {'ci': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include several GitHub actions for Continuous Integration (CI) testing', 'help\_text': 'Nf-core provides a set of Continuous Integration (CI) tests for Github.\nWhen you open a pull request (PR) on your pipeline repository, these tests will run automatically.\n\nThere are different types of tests:\n\* Linting tests check that your code is formatted correctly and that it adheres to nf-core standards\n For code linting they will use [prettier](https://prettier.io/).\n\* Pipeline tests run your pipeline on a small dataset to check that it works\n These tests are run with a small test dataset on GitHub and a larger test dataset on AWS\n\* Marking old issues as stale\n', 'linting': {'files\_exist': \['.github/workflows/branch.yml', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', '.github/workflows/linting\_comment.yml', '.github/workflows/linting.yml']}, 'nfcore\_pipelines': False, 'short\_description': 'Add Github CI tests', 'skippable\_paths': \['.github/workflows/']}, 'nf-test': {'custom\_pipelines': True, 'default': True, 'description': 'Add pipeline testing using nf-test', 'help\_text': "This will add pipeline testing with [nf-test](https://www.nf-test.com/).\n\nWill add and \`nf-test.config\` file setting up the appropriate configuration to test your pipeline.\nOn top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests.\n\nIf you skip this feature, you will still be able to test your pipeline with a \`test\` profile by running the pipeline.\nBut you won't have the automated CI testing.\nYou can add CI by yourself.\n", 'linting': {'files\_exist': \['.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', 'nf-test.config', 'tests/default.nf.test'], 'nf\_test\_content': False}, 'nfcore\_pipelines': False, 'short\_description': 'Add pipeline testing', 'skippable\_paths': \['.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml', 'nf-test.config', 'tests/default.nf.test', 'tests/.nftignore', 'tests/nextflow.config']}, 'test\_config': {'custom\_pipelines': True, 'default': True, 'description': 'Add two default testing profiles', 'help\_text': 'This will add two default testing profiles to run the pipeline with different inputs.\nYou can customise them and add other test profiles.\n\nThese profiles can be used to run the pipeline with a minimal testing dataset with \`nextflow run \ -profile test\`.\n\nThe pipeline will include two profiles: \`test\` and \`test\_full\`.\nIn nf-core, we typically use the \`test\` profile to run the pipeline with a minimal dataset and the \`test\_full\` to run the pipeline with a larger dataset that simulates a real-world scenario.\n', 'linting': {'files\_exist': \['conf/test.config', 'conf/test\_full.config', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml'], 'files\_unchanged': \['.github/PULL\_REQUEST\_TEMPLATE.md'], 'nextflow\_config': False}, 'nfcore\_pipelines': False, 'short\_description': 'Add testing profiles', 'skippable\_paths': \['conf/test.config', 'conf/test\_full.config', '.github/workflows/awsfulltest.yml', '.github/workflows/awstest.yml', '.github/workflows/nf-test.yml', '.github/actions/get-shards/action.yml', '.github/actions/nf-test/action.yml']}}, 'name': 'Continuous Integration & Testing'}, 'development\_environments': {'features': {'codespaces': {'custom\_pipelines': True, 'default': True, 'description': 'The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed.', 'help\_text': 'The pipeline will include a devcontainer configuration.\nThe devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed.\n\nGithub Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal.\n', 'linting': {'files\_unchanged': \['docs/CONTRIBUTING.md']}, 'nfcore\_pipelines': False, 'short\_description': 'Include GitHub Codespaces', 'skippable\_paths': \['.devcontainer/devcontainer.json', '.devcontainer/setup.sh']}, 'vscode': {'custom\_pipelines': True, 'default': True, 'description': 'Add a VSCode configuration to render website admonitions', 'help\_text': 'This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website.\n\nAdds the \`.vscode\` directory to the pipelinerepository.\n', 'nfcore\_pipelines': False, 'short\_description': 'Render website admonitions in VSCode', 'skippable\_paths': \['.vscode']}}, 'name': 'Development Environments'}, 'documentation\_metadata': {'features': {'citations': {'custom\_pipelines': True, 'default': True, 'description': 'Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled).', 'help\_text': 'If adding citations, the pipeline template will contain a \`CITATIONS.md\` file to add the citations of all tools used in the pipeline.\n\nAdditionally, it will include a YAML file (\`assets/methods\_description\_template.yml\`) to add a Materials & Methods section describing the tools used in the pieline,\nand the logics to add this section to the output MultiQC report (if the report is generated).\n', 'linting': {'files\_exist': \['CITATIONS.md']}, 'nfcore\_pipelines': False, 'short\_description': 'Include citations', 'skippable\_paths': \['assets/methods\_description\_template.yml', 'CITATIONS.md']}, 'documentation': {'custom\_pipelines': True, 'default': True, 'description': 'Add documentation to the pipeline', 'help\_text': 'This will add documentation markdown files where you can describe your pipeline.\nIt includes:\n- docs/CONTRIBUTING.md: A contributing guide to help others contribute to your pipeline.\n- docs/README.md: A README file where you can describe the structure of your documentation.\n- docs/output.md: A file where you can explain the output generated by the pipeline\n- docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.\n\nThese files come with an exemplary documentation structure written.\n', 'linting': {'files\_exist': \['docs/CONTRIBUTING.md', 'docs/output.md', 'docs/README.md', 'docs/usage.md']}, 'nfcore\_pipelines': False, 'short\_description': 'Add documentation', 'skippable\_paths': \['docs']}, 'rocrate': {'custom\_pipelines': True, 'default': True, 'description': 'Add a RO-Crate metadata file to describe the pipeline', 'help\_text': 'RO-Crate is a metadata specification to describe research data and software.\nThis will add a \`ro-crate-metadata.json\` file to describe the pipeline.\n', 'linting': {'files\_unchanged': \['.prettierignore'], 'files\_warn': \['ro-crate-metadata.json']}, 'nfcore\_pipelines': False, 'short\_description': 'Add RO-Crate metadata', 'skippable\_paths': \['ro-crate-metadata.json']}}, 'name': 'Documentation & metadata'}, 'notifications': {'features': {'email': {'custom\_pipelines': True, 'default': True, 'description': 'Enable sending emails on pipeline completion.', 'help\_text': 'Enable the option of sending an email which will include pipeline execution reports on pipeline completion.\n', 'linting': {'files\_exist': \['assets/email\_template.html', 'assets/sendmail\_template.txt', 'assets/email\_template.txt'], 'files\_unchanged': \['.prettierignore']}, 'nfcore\_pipelines': False, 'short\_description': 'Enable email updates', 'skippable\_paths': \['assets/email\_template.html', 'assets/sendmail\_template.txt', 'assets/email\_template.txt']}}, 'name': 'Notifications'}, 'repository\_setup': {'features': {'changelog': {'custom\_pipelines': True, 'default': True, 'description': 'Add a CHANGELOG.md file.', 'help\_text': 'Having a \`CHANGELOG.md\` file in the pipeline root directory is useful to track the changes added to each version.\n\nYou can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/\n', 'linting': {'files\_exist': \['CHANGELOG.md']}, 'nfcore\_pipelines': False, 'short\_description': 'Add a changelog', 'skippable\_paths': \['CHANGELOG.md']}, 'github': {'custom\_pipelines': True, 'default': True, 'description': 'Create a GitHub repository for the pipeline.', 'help\_text': 'This will create a GitHub repository for the pipeline.\n\nThe repository will include:\n- Continuous Integration (CI) tests\n- Issues and pull requests templates\n\nThe initialisation of a git repository is required to use the nf-core/tools.\nThis means that even if you unselect this option, your pipeline will still contain a \`.git\` directory and \`.gitignore\` file.\n', 'linting': {'files\_exist': \['.github/ISSUE\_TEMPLATE/bug\_report.yml', '.github/ISSUE\_TEMPLATE/feature\_request.yml', '.github/PULL\_REQUEST\_TEMPLATE.md', '.github/.dockstore.yml', 'docs/CONTRIBUTING.md'], 'files\_unchanged': \['.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/.dockstore.yml'], 'readme': \['nextflow\_badge']}, 'nfcore\_pipelines': False, 'short\_description': 'Use a GitHub repository.', 'skippable\_paths': \['.github', '.gitattributes']}, 'github\_badges': {'custom\_pipelines': True, 'default': True, 'description': 'The README.md file of the pipeline will include GitHub badges', 'help\_text': 'The pipeline \`README.md\` will include badges for:\n\* AWS CI Tests\n\* Zenodo DOI\n\* Nextflow\n\* nf-core template version\n\* Conda\n\* Docker\n\* Singularity\n\* Launching on Nextflow Tower\n', 'linting': {'readme': \['nextflow\_badge', 'nfcore\_template\_badge']}, 'nfcore\_pipelines': False, 'short\_description': 'Add Github badges', 'skippable\_paths': False}, 'license': {'custom\_pipelines': True, 'default': True, 'description': 'Add the MIT license file.', 'help\_text': 'To protect the copyright of the pipeline, you can add a LICENSE file.\nThis option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT\n', 'linting': {'files\_exist': \['LICENSE'], 'files\_unchanged': \['LICENSE']}, 'nfcore\_pipelines': False, 'short\_description': 'Add a license File', 'skippable\_paths': \['LICENSE']}}, 'name': 'Repository Setup'}}_ diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/download.md b/sites/docs/src/content/api_reference/dev/api/pipelines/download.md index e4faa1d066..ee860ce2dc 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/download.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/download.md @@ -1 +1 @@ -# nf_core.pipelines.download +# nf\_core.pipelines.download diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/index.md b/sites/docs/src/content/api_reference/dev/api/pipelines/index.md index 3cfe514e5b..d71c4fe6d5 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/index.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/index.md @@ -1,12 +1,12 @@ # API Reference -- [nf_core.pipelines.bump_version](bump_version) -- [nf_core.pipelines.create](create) -- [nf_core.pipelines.download](download) -- [nf_core.pipelines.launch](launch) -- [nf_core.pipelines.lint](lint) -- [nf_core.pipelines.utils](lint_utils) -- [nf_core.pipelines.list](list) -- [nf_core.pipelines.params_file](params-file) -- [nf_core.pipelines.schema](schema) -- [nf_core.pipelines.sync](sync) +- [nf\_core.pipelines.bump\_version](bump_version) +- [nf\_core.pipelines.create](create) +- [nf\_core.pipelines.download](download) +- [nf\_core.pipelines.launch](launch) +- [nf\_core.pipelines.lint](lint) +- [nf\_core.pipelines.utils](lint_utils) +- [nf\_core.pipelines.list](list) +- [nf\_core.pipelines.params\_file](params-file) +- [nf\_core.pipelines.schema](schema) +- [nf\_core.pipelines.sync](sync) diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/launch.md b/sites/docs/src/content/api_reference/dev/api/pipelines/launch.md index 52b1bd1f56..5b7caeb082 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/launch.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/launch.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.launch +# nf\_core.pipelines.launch Launch a pipeline, interactively collecting params @@ -41,12 +41,12 @@ Take the Nextflow flag schema and merge it with the pipeline schema Prompt for edits to a group of parameters (subschema in ‘definitions’) - **Parameters:** - - **group_id** – Parameter ID (string) - - **group_obj** – JSON Schema keys (dict) + - **group\_id** – Parameter ID (string) + - **group\_obj** – JSON Schema keys (dict) - **Returns:** val answers - **Return type:** - Dict of param_id + Dict of param\_id #### `prompt_param(param_id, param_obj, is_required, answers){:python}` @@ -68,17 +68,17 @@ Use the functions defined in the cli wizard to convert to the correct types. #### `set_schema_inputs(){:python}` Take the loaded schema and set the defaults as the input parameters -If a nf_params.json file is supplied, apply these over the top +If a nf\_params.json file is supplied, apply these over the top #### `single_param_to_questionary(param_id, param_obj, answers=None, print_help=True){:python}` Convert a JSONSchema param to a Questionary question - **Parameters:** - - **param_id** – Parameter ID (string) - - **param_obj** – JSON Schema keys (dict) + - **param\_id** – Parameter ID (string) + - **param\_obj** – JSON Schema keys (dict) - **answers** – Optional preexisting answers (dict) - - **print_help** – If description and help_text should be printed (bool) + - **print\_help** – If description and help\_text should be printed (bool) - **Returns:** Single Questionary dict, to be appended to questions list diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md b/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md index 2324698dbc..a47366e7e4 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/lint.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.lint +# nf\_core.pipelines.lint :::tip See the [Lint Tests]() docs for information about specific linting functions. @@ -18,10 +18,10 @@ in either release mode or normal mode (default). Returns an object of type [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) after finished. - **Parameters:** - - **pipeline_dir** (_str_) – The path to the Nextflow pipeline root directory - - **release_mode** (_bool_) – Set this to True, if the linting should be run in the release mode. + - **pipeline\_dir** (_str_) – The path to the Nextflow pipeline root directory + - **release\_mode** (_bool_) – Set this to True, if the linting should be run in the release mode. See [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) for more information. - - **plain_text** (_bool_) – Print output in plain text without rich formatting + - **plain\_text** (_bool_) – Print output in plain text without rich formatting - **Returns:** An object of type [`PipelineLint`](#nf_core.pipelines.lint.PipelineLint) that contains all the linting results. An object of type `ComponentLint` that contains all the linting results for the modules. @@ -111,7 +111,7 @@ summarising the linting results. Function to dump lint results to a JSON file for downstream use - **Parameters:** - **json_fn** (_str_) – File path to write JSON to. + **json\_fn** (_str_) – File path to write JSON to. #### `_wrap_quotes(files: list[str] | list[Path] | Path) → str{:python}` diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md b/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md index ba916db529..de776516d4 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/lint_utils.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.utils +# nf\_core.pipelines.utils ### `nf_core.pipelines.lint_utils.check_git_repo() → bool{:python}` @@ -7,22 +7,22 @@ Check if the current directory is a git repository. ### `nf_core.pipelines.lint_utils.dump_json_with_prettier(file_name, file_content){:python}` Dump a JSON file and run prettier on it. -:param file_name: A file identifier as a string or pathlib.Path. -:type file_name: Path | str -:param file_content: Content to dump into the JSON file -:type file_content: dict +:param file\_name: A file identifier as a string or pathlib.Path. +:type file\_name: Path | str +:param file\_content: Content to dump into the JSON file +:type file\_content: dict ### `nf_core.pipelines.lint_utils.dump_yaml_with_prettier(file_name: Path | str, file_content: dict) → None{:python}` Dump a YAML file and run prettier on it. - **Parameters:** - - **file_name** (_Path_ _|_ _str_) – A file identifier as a string or pathlib.Path. - - **file_content** (_dict_) – Content to dump into the YAML file + - **file\_name** (_Path_ _|_ _str_) – A file identifier as a string or pathlib.Path. + - **file\_content** (_dict_) – Content to dump into the YAML file ### `nf_core.pipelines.lint_utils.ignore_file(lint_name: str, file_path: Path, dir_path: Path) → list[list[str]]{:python}` -Ignore a file and add the result to the ignored list. Return the passed, failed, ignored and ignore_configs lists. +Ignore a file and add the result to the ignored list. Return the passed, failed, ignored and ignore\_configs lists. ### `nf_core.pipelines.lint_utils.print_fixes(lint_obj, plain_text=False){:python}` @@ -37,18 +37,18 @@ Print a joint summary of the general pipe lint tests and the module and subworkf Print lint results in plain text format. - **Parameters:** - - **results_list** – List of tuples (results, symbol, label, color, show_condition) + - **results\_list** – List of tuples (results, symbol, label, color, show\_condition) - **directory** – Base directory for relative paths (for component linting) - - **component_type** – “modules” or “subworkflows” (for component linting) + - **component\_type** – “modules” or “subworkflows” (for component linting) ### `nf_core.pipelines.lint_utils.print_summary(rows, plain_text=False, summary_colour=None){:python}` Print a summary table in plain text or rich format. - **Parameters:** - - **rows** – List of tuples (count, icon, label, color, always_show) - - **plain_text** – If True, print in plain text format - - **summary_colour** – Color for the rich table border (default: auto based on failures) + - **rows** – List of tuples (count, icon, label, color, always\_show) + - **plain\_text** – If True, print in plain text format + - **summary\_colour** – Color for the rich table border (default: auto based on failures) ### `nf_core.pipelines.lint_utils.run_prettier_on_file(file: Path | str | list[str]) → None{:python}` diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/list.md b/sites/docs/src/content/api_reference/dev/api/pipelines/list.md index 6d537eec7a..f462ef218b 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/list.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/list.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.list +# nf\_core.pipelines.list Lists available nf-core pipelines and versions. @@ -32,8 +32,8 @@ Is used to collect local and remote nf-core pipelines. Pipelines can be sorted, filtered and compared. - **Parameters:** - - **filter_by** (_list_) – A list of strings that can be used for filtering. - - **sort_by** (_str_) – workflows can be sorted by keywords. Keyword must be one of + - **filter\_by** (_list_) – A list of strings that can be used for filtering. + - **sort\_by** (_str_) – workflows can be sorted by keywords. Keyword must be one of release (default), name, stars. #### `compare_remote_local(){:python}` @@ -101,10 +101,10 @@ Check if this workflow has a local copy and use nextflow to pull it if not Prints out a list of all nf-core workflows. - **Parameters:** - - **filter_by** (_list_) – A list of strings that can be used for filtering. - - **sort_by** (_str_) – workflows can be sorted by keywords. Keyword must be one of + - **filter\_by** (_list_) – A list of strings that can be used for filtering. + - **sort\_by** (_str_) – workflows can be sorted by keywords. Keyword must be one of release (default), name, stars. - - **as_json** (_boolean_) – Set to true, if the lists should be printed in JSON. + - **as\_json** (_boolean_) – Set to true, if the lists should be printed in JSON. ### `nf_core.pipelines.list.pretty_date(time){:python}` diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/params-file.md b/sites/docs/src/content/api_reference/dev/api/pipelines/params-file.md index 962dfdabb6..035bc05907 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/params-file.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/params-file.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.params_file +# nf\_core.pipelines.params\_file Create a YAML parameter file @@ -18,7 +18,7 @@ Format a group of parameters of the schema as commented YAML. - **Parameters:** - **definition** (_dict_) – Definition of the group from the schema - - **show_hidden** (_bool_) – Whether to include hidden parameters + - **show\_hidden** (_bool_) – Whether to include hidden parameters - **Returns:** Formatted output for a group - **Return type:** @@ -31,11 +31,11 @@ Format a single parameter of the schema as commented YAML - **Parameters:** - **name** (_str_) – Name of the parameter - **properties** (_dict_) – Properties of the parameter - - **required_properties** (_list_) – List of required properties - - **show_hidden** (_bool_) – Whether to include hidden parameters + - **required\_properties** (_list_) – List of required properties + - **show\_hidden** (_bool_) – Whether to include hidden parameters - **Returns:** Section of a params-file.yml for given parameter - None: If the parameter is skipped because it is hidden and show_hidden is not set + None: If the parameter is skipped because it is hidden and show\_hidden is not set - **Return type:** str @@ -46,7 +46,7 @@ Generate the contents of a parameter template file. Assumes the pipeline has been fetched (if remote) and the schema loaded. - **Parameters:** - **show_hidden** (_bool_) – Whether to include hidden parameters + **show\_hidden** (_bool_) – Whether to include hidden parameters - **Returns:** Formatted output for the pipeline schema - **Return type:** @@ -61,8 +61,8 @@ Prompt the user for a pipeline name and get the schema Build a template file for the pipeline schema. - **Parameters:** - - **output_fn** (_str_ _,_ _optional_) – Filename to write the template to. - - **show_hidden** (_bool_ _,_ _optional_) – Include parameters marked as hidden in the output + - **output\_fn** (_str_ _,_ _optional_) – Filename to write the template to. + - **show\_hidden** (_bool_ _,_ _optional_) – Include parameters marked as hidden in the output - **force** (_bool_ _,_ _optional_) – Whether to overwrite existing output file. - **Returns:** True if the template was written successfully, False otherwise @@ -75,8 +75,8 @@ Helper function to format text for the params-file template. - **Parameters:** - **text** (_str_) – Text to print - - **fill_char** (_str_ _,_ _optional_) – Character to use for creating dividers. Defaults to ‘-‘. + - **fill\_char** (_str_ _,_ _optional_) – Character to use for creating dividers. Defaults to ‘-‘. - **mode** (_str_ _,_ _optional_) – Where to place dividers. Defaults to “both”. - **width** (_int_ _,_ _optional_) – Maximum line-width of the output text. Defaults to 80. - **indent** (_int_ _,_ _optional_) – Number of spaces to indent the text. Defaults to 0. - - **drop_whitespace** (_bool_ _,_ _optional_) – Whether to drop whitespace from the start and end of lines. + - **drop\_whitespace** (_bool_ _,_ _optional_) – Whether to drop whitespace from the start and end of lines. diff --git a/sites/docs/src/content/api_reference/dev/api/pipelines/schema.md b/sites/docs/src/content/api_reference/dev/api/pipelines/schema.md index c098c3cab3..3db16f5474 100644 --- a/sites/docs/src/content/api_reference/dev/api/pipelines/schema.md +++ b/sites/docs/src/content/api_reference/dev/api/pipelines/schema.md @@ -1,4 +1,4 @@ -# nf_core.pipelines.schema +# nf\_core.pipelines.schema Code to deal with pipeline JSON Schema @@ -43,14 +43,14 @@ Common mime types: _ +#### `_abc_impl{:python}`_= <\_abc.\_abc\_data object>_ #### `author{:python}`_: str | None_ @@ -120,14 +120,14 @@ Bases: `BaseModel` .nf-core.yml configuration file schema -#### `_abc_impl{:python}`_= <\_abc.\_abc_data object>_ +#### `_abc_impl{:python}`_= <\_abc.\_abc\_data object>_ #### `bump_version{:python}`_: dict\[str, bool] | None_ //nf-co.re/docs/nf-core-tools/modules/bump-versions for more information. - **Type:** - Disable bumping of the version for a module/subworkflow (when repository_type is modules). See https + Disable bumping of the version for a module/subworkflow (when repository\_type is modules). See https #### `container_registry{:python}`_: list\[str] | None_ @@ -142,38 +142,38 @@ Additional container registry prefixes allowed when linting container directives - **Type:** Pipeline linting configuration, see https -#### `model_config{:python}`_: ClassVar\[ConfigDict]_ _= {'populate_by_name': True, 'validate_by_alias': True, 'validate_by_name': True}_ +#### `model_config{:python}`_: ClassVar\[ConfigDict]_ _= {'populate\_by\_name': True, 'validate\_by\_alias': True, 'validate\_by\_name': True}_ Configuration for the model, should be a dictionary conforming to \[ConfigDict]\[pydantic.config.ConfigDict]. #### `model_dump(**kwargs) → dict[str, Any]{:python}` !!! abstract “Usage Documentation” -: [model_dump](../concepts/serialization#python-mode) +: [model\_dump](../concepts/serialization#python-mode) Generate a dictionary representation of the model, optionally specifying which fields to include or exclude. - **Parameters:** - - **mode** – The mode in which to_python should run. + - **mode** – The mode in which to\_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects. - **include** – A set of fields to include in the output. - **exclude** – A set of fields to exclude from the output. - **context** – Additional context to pass to the serializer. - - **by_alias** – Whether to use the field’s alias in the dictionary key if defined. - - **exclude_unset** – Whether to exclude fields that have not been explicitly set. - - **exclude_defaults** – Whether to exclude fields that are set to their default value. - - **exclude_none** – Whether to exclude fields that have a value of None. - - **exclude_computed_fields** – Whether to exclude computed fields. + - **by\_alias** – Whether to use the field’s alias in the dictionary key if defined. + - **exclude\_unset** – Whether to exclude fields that have not been explicitly set. + - **exclude\_defaults** – Whether to exclude fields that are set to their default value. + - **exclude\_none** – Whether to exclude fields that have a value of None. + - **exclude\_computed\_fields** – Whether to exclude computed fields. While this can be useful for round-tripping, it is usually recommended to use the dedicated - round_trip parameter instead. - - **round_trip** – If True, dumped values should be valid as input for non-idempotent types such as Json\[T]. + round\_trip parameter instead. + - **round\_trip** – If True, dumped values should be valid as input for non-idempotent types such as Json\[T]. - **warnings** – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, - “error” raises a \[PydanticSerializationError]\[pydantic_core.PydanticSerializationError]. + “error” raises a \[PydanticSerializationError]\[pydantic\_core.PydanticSerializationError]. - **fallback** – A function to call when an unknown value is encountered. If not provided, - a \[PydanticSerializationError]\[pydantic_core.PydanticSerializationError] error is raised. - - **serialize_as_any** – Whether to serialize fields with duck-typing serialization behavior. - - **polymorphic_serialization** – Whether to use model and dataclass polymorphic serialization for this call. + a \[PydanticSerializationError]\[pydantic\_core.PydanticSerializationError] error is raised. + - **serialize\_as\_any** – Whether to serialize fields with duck-typing serialization behavior. + - **polymorphic\_serialization** – Whether to use model and dataclass polymorphic serialization for this call. - **Returns:** A dictionary representation of the model. @@ -183,7 +183,7 @@ Version of nf-core/tools used to create/update the pipeline #### `org_path{:python}`_: str | None_ -Path to the organisation’s modules repository (used for modules repo_type only) +Path to the organisation’s modules repository (used for modules repo\_type only) #### `repository_type{:python}`_: Literal\['pipeline', 'modules'] | None_ @@ -198,7 +198,7 @@ Pipeline template configuration //nf-co.re/docs/nf-core-tools/modules/update for more information. - **Type:** - Disable updating specific modules/subworkflows (when repository_type is pipeline). See https + Disable updating specific modules/subworkflows (when repository\_type is pipeline). See https ### _`class{:python}`_`nf_core.utils.NFCoreYamlLintConfig(, files_unchanged: bool | list[str] | None = None, modules_config: bool | list[str] | None = None, merge_markers: bool | list[str] | None = None, nextflow_config: bool | list[str | dict[str, list[str]]] | None = None, nf_test_content: bool | list[str] | None = None, multiqc_config: bool | list[str] | None = None, files_exist: bool | list[str] | None = None, template_strings: bool | list[str] | None = None, readme: bool | list[str] | None = None, nfcore_components: bool | None = None, actions_nf_test: bool | None = None, actions_awstest: bool | None = None, actions_awsfulltest: bool | None = None, pipeline_todos: bool | None = None, pipeline_if_empty_null: bool | None = None, plugin_includes: bool | None = None, pipeline_name_conventions: bool | None = None, schema_lint: bool | None = None, schema_params: bool | None = None, system_exit: bool | None = None, schema_description: bool | None = None, actions_schema_validation: bool | None = None, modules_json: bool | None = None, modules_structure: bool | None = None, base_config: bool | None = None, nfcore_yml: bool | None = None, version_consistency: bool | None = None, included_configs: bool | None = None, local_component_structure: bool | None = None, container_configs: bool | None = None, rocrate_readme_sync: bool | None = None){:python}` @@ -239,7 +239,7 @@ nf_test_content: - nf-test.config ``` -#### `_abc_impl{:python}`_= <\_abc.\_abc_data object>_ +#### `_abc_impl{:python}`_= <\_abc.\_abc\_data object>_ #### `actions_awsfulltest{:python}`_: bool | None_ @@ -353,7 +353,7 @@ Check that every parameter in the schema has a description. #### `schema_lint{:python}`_: bool | None_ -Lint nextflow_schema.json file +Lint nextflow\_schema.json file #### `schema_params{:python}`_: bool | None_ @@ -410,7 +410,7 @@ A list of files found during the linting process. #### `git_sha{:python}` -The git sha for the repo commit / current GitHub pull-request ($GITHUB_PR_COMMIT) +The git sha for the repo commit / current GitHub pull-request ($GITHUB\_PR\_COMMIT) - **Type:** str @@ -491,7 +491,7 @@ Bases: `Validator` Validator for file path specified as –singularity-cache-index argument in nf-core pipelines download -#### `_abc_impl{:python}`_= <\_abc.\_abc_data object>_ +#### `_abc_impl{:python}`_= <\_abc.\_abc\_data object>_ #### `validate(document) → None{:python}` @@ -509,10 +509,10 @@ Sends a HTTP GET request to the Anaconda remote API. - **Parameters:** - **dep** (_str_) – A conda package name. - - **dep_channels** (_list_) – list of conda channels to use + - **dep\_channels** (_list_) – list of conda channels to use - **Raises:** - **A LookupError**\*\*,\*\* **if the connection fails** **or** **times out** **or** **gives an unexpected status code** – - - **A ValueError**\*\*,\*\* **if the package name can not be found** **(\*\***404\***\*)** – + - **A ValueError**\*\*,\*\* **if the package name can not be found** **(****404****)** – ### `nf_core.utils.check_if_outdated(current_version=None, remote_version=None, source_url='https://nf-co.re/tools_version'){:python}` @@ -523,10 +523,10 @@ Check if the current version of nf-core is outdated Check the version of Nextflow installed on the system. - **Parameters:** - - **minimal_nf_version** (_tuple_ \*\[\*_int_ _,_ _int_ _,_ _int_ _,_ _bool_ _]_) – The minimal version of Nextflow required. + - **minimal\_nf\_version** (_tuple_ \*\[\*_int_ _,_ _int_ _,_ _int_ _,_ _bool_ _]_) – The minimal version of Nextflow required. - **silent** (_bool_) – Whether to log the version or not. - **Returns:** - True if the installed version is greater than or equal to minimal_nf_version + True if the installed version is greater than or equal to minimal\_nf\_version - **Return type:** bool @@ -544,8 +544,8 @@ Uses Nextflow to retrieve the the configuration variables from a Nextflow workflow. - **Parameters:** - - **wf_path** (_str_) – Nextflow workflow file system path. - - **cache_config** (_bool_) – cache configuration or not (def. True) + - **wf\_path** (_str_) – Nextflow workflow file system path. + - **cache\_config** (_bool_) – cache configuration or not (def. True) - **Returns:** Workflow configuration settings. - **Return type:** @@ -571,7 +571,7 @@ Returns the most recent container versions by default. - **Raises:** - **A LookupError**\*\*,\*\* **if the connection fails** **or** **times out** **or** **gives an unexpected status code** – - - **A ValueError**\*\*,\*\* **if the package name can not be found** **(\*\***404\***\*)** – + - **A ValueError**\*\*,\*\* **if the package name can not be found** **(****404****)** – ### `nf_core.utils.get_first_available_path(directory: Path | str, paths: list[str]) → Path | None{:python}` @@ -581,15 +581,15 @@ Get the version of Nextflow installed on the system. Cached for the lifetime of ### `nf_core.utils.get_repo_commit(pipeline, commit_id){:python}` -Check if the repo contains the requested commit_id, and expand it to long form if necessary. +Check if the repo contains the requested commit\_id, and expand it to long form if necessary. - **Parameters:** - **pipeline** (_str_) – GitHub repo username/repo - - **commit_id** – The requested commit ID (SHA). It can be in standard long/short form, or any length. + - **commit\_id** – The requested commit ID (SHA). It can be in standard long/short form, or any length. - **Returns:** String or None - **Return type:** - commit_id + commit\_id ### `nf_core.utils.get_repo_releases_branches(pipeline, wfs){:python}` @@ -597,11 +597,11 @@ Fetches details of a nf-core workflow to download. - **Parameters:** - **pipeline** (_str_) – GitHub repo username/repo - - **wfs** – A nf_core.pipelines.list.Workflows() object, where get_remote_workflows() has been called. + - **wfs** – A nf\_core.pipelines.list.Workflows() object, where get\_remote\_workflows() has been called. - **Returns:** Array of releases, Array of branches - **Return type:** - wf_releases, wf_branches (tuple) + wf\_releases, wf\_branches (tuple) - **Raises:** **LockupError**\*\*,\*\* **if the pipeline can not be found.** – @@ -623,7 +623,7 @@ Checks if the specified directory have the minimum required files (‘main.nf’, ‘nextflow.config’) for a pipeline directory - **Parameters:** - **wf_path** (_str_) – The directory to be inspected + **wf\_path** (_str_) – The directory to be inspected - **Raises:** **UserWarning** – If one of the files are missing @@ -631,7 +631,7 @@ Checks if the specified directory have the minimum required files Checks if a path is relative to another. -Should mimic Path.is_relative_to which not available in Python < 3.9 +Should mimic Path.is\_relative\_to which not available in Python < 3.9 path1 (Path | str): The path that could be a subpath path2 (Path | str): The path the could be the superpath @@ -666,7 +666,7 @@ Sets the value in a nested dict using a list of keys to traverse ### `nf_core.utils.parse_anaconda_licence(anaconda_response, version=None){:python}` -Given a response from the anaconda API using anaconda_package, parse the software licences. +Given a response from the anaconda API using anaconda\_package, parse the software licences. Returns: Set of licence types @@ -698,7 +698,7 @@ Return ‘ies’ if the input is not one or has not the length of one, else ‘y Poll the nf-core website API -Takes argument api_url for URL +Takes argument api\_url for URL Expects API response to be valid JSON and contain a top-level ‘status’ key. @@ -709,8 +709,8 @@ Expects API response to be valid JSON and contain a top-level ‘status’ key. Prompt for pipeline release / branch - **Parameters:** - - **wf_releases** (_array_) – Array of repo releases as returned by the GitHub API - - **wf_branches** (_array_) – Array of repo branches, as returned by the GitHub API + - **wf\_releases** (_array_) – Array of repo releases as returned by the GitHub API + - **wf\_branches** (_array_) – Array of repo branches, as returned by the GitHub API - **multiple** (_bool_) – Allow selection of multiple releases & branches (for Seqera Platform) - **Returns:** Selected release / branch or False if no releases / branches available @@ -722,7 +722,7 @@ Prompt for pipeline release / branch Prompt for the pipeline name with questionary - **Parameters:** - **wfs** – A nf_core.pipelines.list.Workflows() object, where get_remote_workflows() has been called. + **wfs** – A nf\_core.pipelines.list.Workflows() object, where get\_remote\_workflows() has been called. - **Returns:** GitHub repo - username/repo - **Return type:** @@ -755,7 +755,7 @@ Context manager to create a tempdir and change into it, ensuring its removal and the original working directory on exit (including exceptions). - **Parameters:** - **base_dir** – Directory in which to create the tempdir. Defaults to the system temp location. + **base\_dir** – Directory in which to create the tempdir. Defaults to the system temp location. ### `nf_core.utils.setup_nfcore_cachedir(cache_fn: str | Path) → Path{:python}` @@ -774,7 +774,7 @@ Sets up local caching for faster remote HTTP requests. Caching directory will be set up in the user’s home directory under a .config/nf-core/cache\_\* subdir. -Uses requests_cache monkey patching. +Uses requests\_cache monkey patching. Also returns the config dict so that we can use the same setup with a Session. ### `nf_core.utils.sort_dictionary(d: dict) → dict{:python}` @@ -791,7 +791,7 @@ From Stack Overflow: Remove paired quotes (single or double) from start and end of string. -Uses ast.literal_eval to safely parse Python string literals, preserving +Uses ast.literal\_eval to safely parse Python string literals, preserving the original string if it’s not a valid literal. Special handling for ruamel.yaml DoubleQuotedScalarString to preserve @@ -807,7 +807,7 @@ strings that should not be converted to numbers (e.g., “123” stays as string Validates the md5 checksum of a file on disk. - **Parameters:** - - **file_name** (_str_) – Path to a local file. + - **file\_name** (_str_) – Path to a local file. - **expected** (_str_) – The expected md5sum. - **Raises:** **IOError**\*\*,\*\* **if the md5sum does not match the remote sum.** – @@ -819,7 +819,7 @@ Display a command-line spinner while calling a function repeatedly. Keep waiting until that function returns True - **Parameters:** - - **poll_func** (_function_) – Function to call - - **refresh_per_second** (_int_) – Refresh this many times per second. Default: 20. + - **poll\_func** (_function_) – Function to call + - **refresh\_per\_second** (_int_) – Refresh this many times per second. Default: 20. - **Returns:** None. Just sits in an infinite loop until the function returns True. diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md index 43866a3db0..8a8a1f77e5 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md @@ -1,4 +1,4 @@ -# environment_yml +# environment\_yml #### `ModuleLint.environment_yml(module: NFCoreComponent, allow_missing: bool = False, fix_version: bool = False, progress_bar: Progress | None = None) → None{:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md index bb8f8817a8..e95485b3ab 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md @@ -1,4 +1,4 @@ -# main_nf +# main\_nf #### `ModuleLint.main_nf(module: NFCoreComponent, fix_version: bool, registry: tuple[str, ...], progress_bar: Progress) → tuple[list[str], list[str]]{:python}` @@ -21,6 +21,15 @@ The following checks are performed: are specified, their tags must reference the same software version. A warning is issued if they do not match. Modules using the newer docker-only format (no singularity container) skip this check. +- `singularity_tag`: A Singularity container must be resolvable via + `nextflow inspect -profile singularity`. The check fails if none can be + resolved or if it falls back to a docker container that has an automatic + singularity equivalent, i.e., `quay.io/biocontainers/` or + `community.wave.seqera.io/`. + It is skipped for modules listed under `singularity` in `.github/skip_nf_test.json`. +- `oras_singularity_tag`: The resolved Singularity container must not be + served over the `oras://` scheme; it should be a plain `https://` URL. + The check fails if an `oras://` container is used. - `main_nf_script_shell`: Exactly one of `script:`, `shell:`, or `exec:` blocks must be present. - `main_nf_shell_template`: If a `shell:` block is used, it must call diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md index e577862aad..3b6d8e5ab5 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md @@ -1,4 +1,4 @@ -# meta_yml +# meta\_yml #### `ModuleLint.meta_yml(module: NFCoreComponent, allow_missing: bool = False) → None{:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_changes.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_changes.md index f02be1a3ed..814c8ec4e8 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_changes.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_changes.md @@ -1,4 +1,4 @@ -# module_changes +# module\_changes #### `ModuleLint.module_changes(module){:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_deprecations.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_deprecations.md index 94d115eb22..03c5e279d8 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_deprecations.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_deprecations.md @@ -1,4 +1,4 @@ -# module_deprecations +# module\_deprecations #### `ModuleLint.module_deprecations(module){:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_patch.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_patch.md index 5d38a40d31..56e72c0b7f 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_patch.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_patch.md @@ -1,4 +1,4 @@ -# module_patch +# module\_patch #### `ModuleLint.module_patch(module: NFCoreComponent){:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md index 221aa67f3e..20ba950e56 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md @@ -1,4 +1,4 @@ -# module_tests +# module\_tests #### `ModuleLint.module_tests(module: NFCoreComponent, allow_missing: bool = False){:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_todos.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_todos.md index b342e2d098..9553cd435a 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_todos.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_todos.md @@ -1,4 +1,4 @@ -# module_todos +# module\_todos #### `ModuleLint.module_todos(module){:python}` diff --git a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_version.md b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_version.md index 68c6fbf8e1..5ccfb1777a 100644 --- a/sites/docs/src/content/api_reference/dev/module_lint_tests/module_version.md +++ b/sites/docs/src/content/api_reference/dev/module_lint_tests/module_version.md @@ -1,4 +1,4 @@ -# module_version +# module\_version #### `ModuleLint.module_version(module: NFCoreComponent){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awsfulltest.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awsfulltest.md index f24ae81f03..6647ea7597 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awsfulltest.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awsfulltest.md @@ -1,4 +1,4 @@ -# actions_awsfulltest +# actions\_awsfulltest #### `PipelineLint.actions_awsfulltest() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awstest.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awstest.md index 4e4698c4e9..5641721c0d 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awstest.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_awstest.md @@ -1,4 +1,4 @@ -# actions_awstest +# actions\_awstest #### `PipelineLint.actions_awstest(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md index f6efdf6b91..a16f70ace0 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_ci.md @@ -1,4 +1,4 @@ -# actions_ci +# actions\_ci #### `PipelineLint.actions_ci(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_nf_test.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_nf_test.md index 37b502339e..623bb19e07 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_nf_test.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_nf_test.md @@ -1,4 +1,4 @@ -# actions_nf_test +# actions\_nf\_test #### `PipelineLint.actions_nf_test(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_schema_validation.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_schema_validation.md index 5c8c647f76..a0a98b5a80 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_schema_validation.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/actions_schema_validation.md @@ -1,4 +1,4 @@ -# actions_schema_validation +# actions\_schema\_validation #### `PipelineLint.actions_schema_validation() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/base_config.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/base_config.md index 73ac2852a2..f1843c1d84 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/base_config.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/base_config.md @@ -1,4 +1,4 @@ -# base_config +# base\_config #### `PipelineLint.base_config() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/container_configs.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/container_configs.md index 9bab2fbc5e..01e59731a9 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/container_configs.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/container_configs.md @@ -1,4 +1,4 @@ -# container_configs +# container\_configs #### `PipelineLint.container_configs(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_exist.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_exist.md index 9cc1480b12..50d353758f 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_exist.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_exist.md @@ -1,4 +1,4 @@ -# files_exist +# files\_exist #### `PipelineLint.files_exist() → dict[str, list[str]]{:python}` @@ -110,5 +110,5 @@ the `files_exist` key as follows in your `.nf-core.yml` config file. For example ::: lint: -: files_exist: -: - assets/multiqc_config.yml +: files\_exist: +: - assets/multiqc\_config.yml diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_unchanged.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_unchanged.md index 9ee5e64659..22bd34dba9 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_unchanged.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/files_unchanged.md @@ -1,4 +1,4 @@ -# files_unchanged +# files\_unchanged #### `PipelineLint.files_unchanged() → dict[str, list[str] | bool]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/included_configs.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/included_configs.md index 146dbc4d79..56e4cb81b0 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/included_configs.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/included_configs.md @@ -1,4 +1,4 @@ -# included_configs +# included\_configs #### `PipelineLint.included_configs(){:python}` @@ -11,4 +11,4 @@ If the include line is missing, the test warns. Can be skipped by adding the following to the .nf-core.yml file: lint: -> included_configs: False +> included\_configs: False diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md index 3601f1803f..df2b8d86a1 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md @@ -1,4 +1,4 @@ -# modules_structure +# modules\_structure #### `PipelineLint.local_component_structure(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/merge_markers.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/merge_markers.md index 2f6aef0aa4..eb62f8cc99 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/merge_markers.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/merge_markers.md @@ -1,4 +1,4 @@ -# merge_markers +# merge\_markers #### `PipelineLint.merge_markers(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_config.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_config.md index 836c2d6087..2ba4459b39 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_config.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_config.md @@ -1,4 +1,4 @@ -# modules_config +# modules\_config #### `PipelineLint.modules_config() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_json.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_json.md index 7019bdba53..a8482c6427 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_json.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_json.md @@ -1,4 +1,4 @@ -# modules_json +# modules\_json #### `PipelineLint.modules_json() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_structure.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_structure.md index 4e08c24956..0aedfc9c80 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_structure.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/modules_structure.md @@ -1,4 +1,4 @@ -# modules_structure +# modules\_structure #### `PipelineLint.modules_structure(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/multiqc_config.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/multiqc_config.md index 5759c80b94..4826fdcdee 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/multiqc_config.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/multiqc_config.md @@ -1,4 +1,4 @@ -# multiqc_config +# multiqc\_config #### `PipelineLint.multiqc_config() → dict[str, list[str]]{:python}` @@ -37,6 +37,6 @@ For example: ``` lint: -: multiqc_config: -: - report_section_order -\- report_comment +: multiqc\_config: +: - report\_section\_order +\- report\_comment diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nextflow_config.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nextflow_config.md index eff2a1ed2c..b65abbdb2a 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nextflow_config.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nextflow_config.md @@ -1,4 +1,4 @@ -# nextflow_config +# nextflow\_config #### `PipelineLint.nextflow_config() → dict[str, list[str]]{:python}` @@ -96,7 +96,7 @@ lint: - A `test` configuration profile should exist. -**The default values in \`\`nextflow.config\`\` should match the default values defined in the \`\`nextflow_schema.json\`\`.** +**The default values in \`\`nextflow.config\`\` should match the default values defined in the \`\`nextflow\_schema.json\`\`.** :::note You can choose to ignore tests for the default value of an specific parameter diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nf_test_content.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nf_test_content.md index a301b1029a..6671e84488 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nf_test_content.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nf_test_content.md @@ -1,4 +1,4 @@ -# nf_test_content +# nf\_test\_content #### `PipelineLint.nf_test_content() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md index cc89afd887..a1c93267c2 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/nfcore_yml.md @@ -1,4 +1,4 @@ -# nfcore_yml +# nfcore\_yml #### `PipelineLint.nfcore_yml() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_if_empty_null.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_if_empty_null.md index 44a167e65e..834e9d0430 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_if_empty_null.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_if_empty_null.md @@ -1,4 +1,4 @@ -# pipeline_if_empty_null +# pipeline\_if\_empty\_null #### `PipelineLint.pipeline_if_empty_null(root_dir=None){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_name_conventions.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_name_conventions.md index 788d77e41a..3ff2f24908 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_name_conventions.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_name_conventions.md @@ -1,4 +1,4 @@ -# pipeline_name_conventions +# pipeline\_name\_conventions #### `PipelineLint.pipeline_name_conventions(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_todos.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_todos.md index ea401161ac..28d19e082e 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_todos.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_todos.md @@ -1,4 +1,4 @@ -# pipeline_todos +# pipeline\_todos #### `PipelineLint.pipeline_todos(root_dir=None){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/plugin_includes.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/plugin_includes.md index 2fa6197af6..b0f7c12a31 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/plugin_includes.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/plugin_includes.md @@ -1,4 +1,4 @@ -# plugin_includes +# plugin\_includes #### `PipelineLint.plugin_includes() → dict[str, list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/rocrate_readme_sync.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/rocrate_readme_sync.md index c34d2175ec..d7c78087ee 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/rocrate_readme_sync.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/rocrate_readme_sync.md @@ -1,4 +1,4 @@ -# rocrate_readme_sync +# rocrate\_readme\_sync #### `PipelineLint.rocrate_readme_sync(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_description.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_description.md index 762ad42ebd..3e9c7c3c0e 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_description.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_description.md @@ -1,4 +1,4 @@ -# schema_description +# schema\_description #### `PipelineLint.schema_description(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_lint.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_lint.md index 43232faf73..7db82c497d 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_lint.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_lint.md @@ -1,4 +1,4 @@ -# schema_lint +# schema\_lint #### `PipelineLint.schema_lint(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_params.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_params.md index 7d9440fa15..3579e37640 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_params.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/schema_params.md @@ -1,4 +1,4 @@ -# schema_params +# schema\_params #### `PipelineLint.schema_params(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/system_exit.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/system_exit.md index dc54311edc..93001ccd24 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/system_exit.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/system_exit.md @@ -1,4 +1,4 @@ -# system_exit +# system\_exit #### `PipelineLint.system_exit(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/template_strings.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/template_strings.md index 364674d06f..da6c0df775 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/template_strings.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/template_strings.md @@ -1,4 +1,4 @@ -# template_strings +# template\_strings #### `PipelineLint.template_strings(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/version_consistency.md b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/version_consistency.md index c5dbb3f426..f0c6f540d0 100644 --- a/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/version_consistency.md +++ b/sites/docs/src/content/api_reference/dev/pipeline_lint_tests/version_consistency.md @@ -1,4 +1,4 @@ -# version_consistency +# version\_consistency #### `PipelineLint.version_consistency(){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/main_nf.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/main_nf.md index bc28949013..848e3af927 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/main_nf.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/main_nf.md @@ -1,4 +1,4 @@ -# main_nf +# main\_nf #### `SubworkflowLint.main_nf(subworkflow: NFCoreComponent) → tuple[list[str], list[str]]{:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/meta_yml.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/meta_yml.md index 230f15dc64..8a06bf6499 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/meta_yml.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/meta_yml.md @@ -1,4 +1,4 @@ -# meta_yml +# meta\_yml #### `SubworkflowLint.meta_yml(subworkflow, allow_missing: bool = False){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_changes.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_changes.md index d167098c87..7bb6fb30f7 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_changes.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_changes.md @@ -1,4 +1,4 @@ -# subworkflow_changes +# subworkflow\_changes #### `SubworkflowLint.subworkflow_changes(subworkflow){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_if_empty_null.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_if_empty_null.md index 28385535fd..537b7ec408 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_if_empty_null.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_if_empty_null.md @@ -1,4 +1,4 @@ -# subworkflow_if_empty_null +# subworkflow\_if\_empty\_null #### `SubworkflowLint.subworkflow_if_empty_null(subworkflow){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md index 3845a1f1a5..2e323c02e5 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md @@ -1,4 +1,4 @@ -# subworkflow_tests +# subworkflow\_tests #### `SubworkflowLint.subworkflow_tests(subworkflow: NFCoreComponent, allow_missing: bool = False){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_todos.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_todos.md index 90e8234278..a0b6bf3ee7 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_todos.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_todos.md @@ -1,4 +1,4 @@ -# subworkflow_todos +# subworkflow\_todos #### `SubworkflowLint.subworkflow_todos(subworkflow){:python}` diff --git a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_version.md b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_version.md index 5ac782926e..23822e9ff6 100644 --- a/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_version.md +++ b/sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_version.md @@ -1,4 +1,4 @@ -# subworkflow_version +# subworkflow\_version #### `SubworkflowLint.subworkflow_version(subworkflow){:python}`