Update nf-core/tools API docs for dev

sites/docs/src/content/api_reference/dev/api/utils.md

@@ -707,6 +707,18 @@ Bases: `BaseModel`
                "default": null,
                "title": "Pipeline Todos"
             },
+            "pipeline_if_empty_null": {
+               "anyOf": [
+                  {
+                     "type": "boolean"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Pipeline If Empty Null"
+            },
             "plugin_includes": {
                "anyOf": [
                   {
@@ -862,6 +874,18 @@ Bases: `BaseModel`
                ],
                "default": null,
                "title": "Included Configs"
+            },
+            "local_component_structure": {
+               "anyOf": [
+                  {
+                     "type": "boolean"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Local Component Structure"
             }
          },
          "title": "NFCoreYamlLintConfig",
@@ -1168,6 +1192,18 @@ schema for linting config in .nf-core.yml should cover:
          "default": null,
          "title": "Pipeline Todos"
       },
+      "pipeline_if_empty_null": {
+         "anyOf": [
+            {
+               "type": "boolean"
+            },
+            {
+               "type": "null"
+            }
+         ],
+         "default": null,
+         "title": "Pipeline If Empty Null"
+      },
       "plugin_includes": {
          "anyOf": [
             {
@@ -1323,6 +1359,18 @@ schema for linting config in .nf-core.yml should cover:
          ],
          "default": null,
          "title": "Included Configs"
+      },
+      "local_component_structure": {
+         "anyOf": [
+            {
+               "type": "boolean"
+            },
+            {
+               "type": "null"
+            }
+         ],
+         "default": null,
+         "title": "Local Component Structure"
       }
    }
 }
@@ -1338,6 +1386,7 @@ schema for linting config in .nf-core.yml should cover:
   - [`files_exist (bool | List[str] | None)`](#nf_core.utils.NFCoreYamlLintConfig.files_exist)
   - [`files_unchanged (bool | List[str] | None)`](#nf_core.utils.NFCoreYamlLintConfig.files_unchanged)
   - [`included_configs (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.included_configs)
+  - [`local_component_structure (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.local_component_structure)
   - [`merge_markers (bool | List[str] | None)`](#nf_core.utils.NFCoreYamlLintConfig.merge_markers)
   - [`modules_config (bool | List[str] | None)`](#nf_core.utils.NFCoreYamlLintConfig.modules_config)
   - [`modules_json (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.modules_json)
@@ -1346,6 +1395,7 @@ schema for linting config in .nf-core.yml should cover:
   - [`nextflow_config (bool | List[str | Dict[str, List[str]]] | None)`](#nf_core.utils.NFCoreYamlLintConfig.nextflow_config)
   - [`nfcore_components (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.nfcore_components)
   - [`nfcore_yml (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.nfcore_yml)
+  - [`pipeline_if_empty_null (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.pipeline_if_empty_null)
   - [`pipeline_name_conventions (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.pipeline_name_conventions)
   - [`pipeline_todos (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.pipeline_todos)
   - [`plugin_includes (bool | None)`](#nf_core.utils.NFCoreYamlLintConfig.plugin_includes)
@@ -1389,6 +1439,10 @@ List of files that should not be changed
 
 Lint for included configs
 
+#### _`field{:python}`_`local_component_structure{:python}`_: bool | None_`{:python}`_= None_
+
+Lint local components use correct structure mirroring remote
+
 #### _`field{:python}`_`merge_markers{:python}`_: bool | List\[str] | None_`{:python}`_= None_
 
 List of files that should not contain merge markers
@@ -1421,6 +1475,10 @@ Lint all required files to use nf-core modules and subworkflows
 
 Lint nf-core.yml
 
+#### _`field{:python}`_`pipeline_if_empty_null{:python}`_: bool | None_`{:python}`_= None_
+
+Lint for ifEmpty(null) statements
+
 #### _`field{:python}`_`pipeline_name_conventions{:python}`_: bool | None_`{:python}`_= None_
 
 Lint for pipeline name conventions

sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md

@@ -1,6 +1,6 @@
 # environment_yml
 
-#### `ModuleLint.environment_yml(module: NFCoreComponent) → None{:python}`
+#### `ModuleLint.environment_yml(module: NFCoreComponent, allow_missing: bool = False) → None{:python}`
 
 Lint an `environment.yml` file.
 

sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md

@@ -1,6 +1,6 @@
 # meta_yml
 
-#### `ModuleLint.meta_yml(module: NFCoreComponent) → None{:python}`
+#### `ModuleLint.meta_yml(module: NFCoreComponent, allow_missing: bool = False) → None{:python}`
 
 Lint a `meta.yml` file
 

sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md

@@ -1,6 +1,6 @@
 # module_tests
 
-#### `ModuleLint.module_tests(module: NFCoreComponent){:python}`
+#### `ModuleLint.module_tests(module: NFCoreComponent, allow_missing: bool = False){:python}`
 
 Lint the tests of a module in `nf-core/modules`
 

sites/docs/src/content/api_reference/dev/pipeline_lint_tests/index.md

@@ -18,6 +18,7 @@
 - [nfcore_yml](./nfcore_yml/)
 - [pipeline_name_conventions](./pipeline_name_conventions/)
 - [pipeline_todos](./pipeline_todos/)
+- [pipeline_if_empty_null](./pipeline_if_empty_null/)
 - [plugin_includes](./plugin_includes/)
 - [readme](./readme/)
 - [schema_description](./schema_description/)

sites/docs/src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md

@@ -0,0 +1,15 @@
+# modules_structure
+
+#### `PipelineLint.local_component_structure(){:python}`
+
+Check that the local modules and subworkflows directories in a pipeline have the correct format:
+
+```bash
+modules/local/TOOL/SUBTOOL
+```
+
+Prior to nf-core/tools release 3.1.0 the directory structure allowed top-level \*.nf files:
+
+```bash
+modules/local/modules/TOOL_SUBTOOL.nf
+```

sites/docs/src/content/api_reference/dev/pipeline_lint_tests/pipeline_if_empty_null.md

@@ -0,0 +1,12 @@
+# pipeline_if_empty_null
+
+#### `PipelineLint.pipeline_if_empty_null(root_dir=None){:python}`
+
+Check for ifEmpty(null)
+
+There are two general cases for workflows to use the channel operator ifEmpty:
+: 1. ifEmpty( \[ ] ) to ensure a process executes, for example when an input file is optional (although this can be replaced by toList()).
+2\. When a channel should not be empty and throws an error ifEmpty { error … }, e.g. reading from an empty samplesheet.
+
+There are multiple examples of workflows that inject null objects into channels using ifEmpty(null), which can cause unhandled null pointer exceptions.
+This lint test throws warnings for those instances.

sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/index.md

@@ -6,5 +6,6 @@
 - [subworkflow_changes](./subworkflow_changes/)
 - [subworkflow_tests](./subworkflow_tests/)
 - [subworkflow_todos](./subworkflow_todos/)
+- [subworkflow_if_empty_null](./subworkflow_if_empty_null/)
 - [subworkflow_version](./subworkflow_version/)
 ```

sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/meta_yml.md

@@ -1,6 +1,6 @@
 # meta_yml
 
-#### `SubworkflowLint.meta_yml(subworkflow){:python}`
+#### `SubworkflowLint.meta_yml(subworkflow, allow_missing: bool = False){:python}`
 
 Lint a `meta.yml` file
 

sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_if_empty_null.md

@@ -0,0 +1,12 @@
+# subworkflow_if_empty_null
+
+#### `SubworkflowLint.subworkflow_if_empty_null(subworkflow){:python}`
+
+Check for ifEmpty(null)
+
+There are two general cases for workflows to use the channel operator ifEmpty:
+: 1. ifEmpty( \[ ] ) to ensure a process executes, for example when an input file is optional (although this can be replaced by toList()).
+2\. When a channel should not be empty and throws an error ifEmpty { error … }, e.g. reading from an empty samplesheet.
+
+There are multiple examples of workflows that inject null objects into channels using ifEmpty(null), which can cause unhandled null pointer exceptions.
+This lint test throws warnings for those instances.

sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md

@@ -1,6 +1,6 @@
 # subworkflow_tests
 
-#### `SubworkflowLint.subworkflow_tests(subworkflow: NFCoreComponent){:python}`
+#### `SubworkflowLint.subworkflow_tests(subworkflow: NFCoreComponent, allow_missing: bool = False){:python}`
 
 Lint the tests of a subworkflow in `nf-core/modules`