[automated] Update nf-core/tools API docs for dev

nf-core · Jan 27, 2025 · 2da6b63 · 2da6b63
1 parent e6771ac
commit 2da6b63
Show file tree

Hide file tree

Showing 7 changed files with 49 additions and 5 deletions.
diff --git a/sites/docs/src/content/api_reference/dev/api/utils.md b/sites/docs/src/content/api_reference/dev/api/utils.md
@@ -862,6 +862,18 @@ Bases: `BaseModel`
                ],
                "default": null,
                "title": "Included Configs"
+            },
+            "local_component_structure": {
+               "anyOf": [
+                  {
+                     "type": "boolean"
+                  },
+                  {
+                     "type": "null"
+                  }
+               ],
+               "default": null,
+               "title": "Local Component Structure"
             }
          },
          "title": "NFCoreYamlLintConfig",
@@ -1323,6 +1335,18 @@ 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 +1362,7 @@ 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)
@@ -1389,6 +1414,10 @@ 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

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
@@ -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.
 

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
@@ -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
 

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
@@ -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`
 

diff --git a/.../src/content/api_reference/dev/pipeline_lint_tests/local_component_structure.md b/.../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
+```
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
@@ -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
 

diff --git a/.../docs/src/content/api_reference/dev/subworkflow_lint_tests/subworkflow_tests.md b/.../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`