Update nf-core/tools API docs for dev

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 <https://nf-co.re/docs/nf-core-tools/modules/bump-versions> for more information.
+Disable bumping of the version for a module/subworkflow (when repository\_type is modules). See <https://nf-co.re/docs/nf-core-tools/modules/bump-versions> 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 <https://nf-co.re/docs/nf-core-tools/modules/update> for more information.
+Disable updating specific modules/subworkflows (when repository\_type is pipeline). See <https://nf-co.re/docs/nf-core-tools/modules/update> 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_
 

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.

sites/docs/src/content/api_reference/dev/api/pipelines/download.md

@@ -1 +1 @@
-# nf_core.pipelines.download
+# nf\_core.pipelines.download

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)

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
 

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}`