diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58e9a36bf3..23fcb83362 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -45,6 +45,7 @@
 - Update gitpod/workspace-base Docker digest to 0f38224 ([#3048](https://github.com/nf-core/tools/pull/3048))
 - update output_dir for api docs to new website structure ([#3051](https://github.com/nf-core/tools/pull/3051))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 ([#3052](https://github.com/nf-core/tools/pull/3052))
+- update api docs to new structure ([#3054](https://github.com/nf-core/tools/pull/3054))
 
 ## [v2.14.1 - Tantalum Toad - Patch](https://github.com/nf-core/tools/releases/tag/2.14.1) - [2024-05-09]
 
diff --git a/docs/api/_src/_static/css/custom.css b/docs/api/_src/_static/css/custom.css
deleted file mode 100644
index e892dd9998..0000000000
--- a/docs/api/_src/_static/css/custom.css
+++ /dev/null
@@ -1,437 +0,0 @@
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-  a,
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-    color: #246eb9;
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-  a:hover,
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-    background-color: #32ad65;
-  }
-  .wy-menu-vertical a {
-    color: #343434;
-  }
-  .wy-menu-vertical a:hover {
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-  }
-  .wy-menu-vertical header,
-  .wy-menu-vertical p.caption {
-    color: #32ad65;
-  }
-
-  .wy-side-nav-search input[type="text"] {
-    border: none;
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-  .rst-content .note .admonition-title {
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-  }
-
-  html.writer-html4 .rst-content dl:not(.docutils) > dt,
-  html.writer-html5
-    .rst-content
-    dl[class]:not(.option-list):not(.field-list):not(.footnote):not(.glossary):not(.simple)
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-  .rst-content .wy-alert-warning.tip .wy-alert-title,
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-  .wy-alert.wy-alert-warning .rst-content .admonition-title,
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-    background-color: #246eb9;
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-  .wy-alert.wy-alert-warning {
-    color: #343434;
-    background-color: #e3e3e3;
-  }
-}
-@media (prefers-color-scheme: dark) {
-  .wy-nav-content-wrap {
-    background-color: #181a1b;
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-  .wy-nav-top,
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-    background-color: #2e2e2e;
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-  .wy-nav-content {
-    background-color: #343434;
-    color: #e5e6e7;
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-    color: #6fb2e8;
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-  html.writer-html5
-    .rst-content
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-  html.writer-html4 .rst-content dl:not(.docutils) dl:not(.field-list) > dt,
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-    .rst-content
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diff --git a/docs/api/_src/_static/js/custom.js b/docs/api/_src/_static/js/custom.js
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/docs/api/_src/_static/nf-core-logo.png b/docs/api/_src/_static/nf-core-logo.png
deleted file mode 100644
index 91ddb58d8a..0000000000
Binary files a/docs/api/_src/_static/nf-core-logo.png and /dev/null differ
diff --git a/docs/api/_src/_templates/layout.html b/docs/api/_src/_templates/layout.html
deleted file mode 100644
index 42341a97c1..0000000000
--- a/docs/api/_src/_templates/layout.html
+++ /dev/null
@@ -1,4 +0,0 @@
-{% extends '!layout.html' %} {% block header %}
-<!-- your html code here -->
-<a href="https://nf-co.re"><img src="./_static/nf-core-logo.png" width="20%" /></a>
-{% endblock %}
diff --git a/docs/api/_src/api/index.md b/docs/api/_src/api/index.md
index a1863f7e39..035a896888 100644
--- a/docs/api/_src/api/index.md
+++ b/docs/api/_src/api/index.md
@@ -1,8 +1,11 @@
-# API Reference
+# nf-core/tools documentation
 
-```{toctree}
-:glob: true
-:maxdepth: 1
+This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.
 
-*
-```
+## Contents
+
+- [Pipeline commands](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
+- [Module commands](./module_lint_tests/) (run by `nf-core modules lint`)
+- [Subworkflow commands](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference](./api/)
+  - [nf-core/tools pipeline commands API referece](./api/pipelines/)
diff --git a/docs/api/_src/api/licences.md b/docs/api/_src/api/licences.md
deleted file mode 100644
index 95b5f9768b..0000000000
--- a/docs/api/_src/api/licences.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.licences
-
-```{eval-rst}
-.. automodule:: nf_core.licences
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/api/modules.md b/docs/api/_src/api/modules.md
deleted file mode 100644
index e3f1e39bed..0000000000
--- a/docs/api/_src/api/modules.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.modules
-
-```{eval-rst}
-.. automodule:: nf_core.modules
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/api/bump_version.md b/docs/api/_src/api/pipelines/bump_version.md
similarity index 72%
rename from docs/api/_src/api/bump_version.md
rename to docs/api/_src/api/pipelines/bump_version.md
index 54c3774408..cd7dc280f6 100644
--- a/docs/api/_src/api/bump_version.md
+++ b/docs/api/_src/api/pipelines/bump_version.md
@@ -1,7 +1,7 @@
 # nf_core.bump_version
 
 ```{eval-rst}
-.. automodule:: nf_core.bump_version
+.. automodule:: nf_core.pipelines.bump_version
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/create.md b/docs/api/_src/api/pipelines/create.md
similarity index 73%
rename from docs/api/_src/api/create.md
rename to docs/api/_src/api/pipelines/create.md
index 5d5f6a62d1..576335e951 100644
--- a/docs/api/_src/api/create.md
+++ b/docs/api/_src/api/pipelines/create.md
@@ -1,7 +1,7 @@
 # nf_core.create
 
 ```{eval-rst}
-.. automodule:: nf_core.create
+.. automodule:: nf_core.pipelines.create
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/download.md b/docs/api/_src/api/pipelines/download.md
similarity index 73%
rename from docs/api/_src/api/download.md
rename to docs/api/_src/api/pipelines/download.md
index 18ab51376e..540fb92c49 100644
--- a/docs/api/_src/api/download.md
+++ b/docs/api/_src/api/pipelines/download.md
@@ -1,7 +1,7 @@
 # nf_core.download
 
 ```{eval-rst}
-.. automodule:: nf_core.download
+.. automodule:: nf_core.pipelines.download
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/pipelines/index.md b/docs/api/_src/api/pipelines/index.md
new file mode 100644
index 0000000000..a1863f7e39
--- /dev/null
+++ b/docs/api/_src/api/pipelines/index.md
@@ -0,0 +1,8 @@
+# API Reference
+
+```{toctree}
+:glob: true
+:maxdepth: 1
+
+*
+```
diff --git a/docs/api/_src/api/launch.md b/docs/api/_src/api/pipelines/launch.md
similarity index 73%
rename from docs/api/_src/api/launch.md
rename to docs/api/_src/api/pipelines/launch.md
index eef777ca87..0f7fc03f64 100644
--- a/docs/api/_src/api/launch.md
+++ b/docs/api/_src/api/pipelines/launch.md
@@ -1,7 +1,7 @@
 # nf_core.launch
 
 ```{eval-rst}
-.. automodule:: nf_core.launch
+.. automodule:: nf_core.pipelines.launch
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/lint.md b/docs/api/_src/api/pipelines/lint.md
similarity index 64%
rename from docs/api/_src/api/lint.md
rename to docs/api/_src/api/pipelines/lint.md
index 1380f7ec7b..aa62c404b8 100644
--- a/docs/api/_src/api/lint.md
+++ b/docs/api/_src/api/pipelines/lint.md
@@ -1,11 +1,11 @@
 # nf_core.lint
 
 :::{seealso}
-See the [Lint Tests](../pipeline_lint_tests/index.md) docs for information about specific linting functions.
+See the [Lint Tests](/docs/nf-core-tools/api_reference/dev/pipeline_lint_tests) docs for information about specific linting functions.
 :::
 
 ```{eval-rst}
-.. automodule:: nf_core.lint
+.. automodule:: nf_core.pipelines.lint
     :members: run_linting
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/list.md b/docs/api/_src/api/pipelines/list.md
similarity index 74%
rename from docs/api/_src/api/list.md
rename to docs/api/_src/api/pipelines/list.md
index 35c819bc56..7df7564544 100644
--- a/docs/api/_src/api/list.md
+++ b/docs/api/_src/api/pipelines/list.md
@@ -1,7 +1,7 @@
 # nf_core.list
 
 ```{eval-rst}
-.. automodule:: nf_core.list
+.. automodule:: nf_core.pipelines.list
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/params-file.md b/docs/api/_src/api/pipelines/params-file.md
similarity index 72%
rename from docs/api/_src/api/params-file.md
rename to docs/api/_src/api/pipelines/params-file.md
index c5bbfc0f1f..06f27cc592 100644
--- a/docs/api/_src/api/params-file.md
+++ b/docs/api/_src/api/pipelines/params-file.md
@@ -1,7 +1,7 @@
 # nf_core.params_file
 
 ```{eval-rst}
-.. automodule:: nf_core.params_file
+.. automodule:: nf_core.pipelines.params_file
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/schema.md b/docs/api/_src/api/pipelines/schema.md
similarity index 73%
rename from docs/api/_src/api/schema.md
rename to docs/api/_src/api/pipelines/schema.md
index a702d28058..c885d9ed23 100644
--- a/docs/api/_src/api/schema.md
+++ b/docs/api/_src/api/pipelines/schema.md
@@ -1,7 +1,7 @@
 # nf_core.schema
 
 ```{eval-rst}
-.. automodule:: nf_core.schema
+.. automodule:: nf_core.pipelines.schema
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/sync.md b/docs/api/_src/api/pipelines/sync.md
similarity index 74%
rename from docs/api/_src/api/sync.md
rename to docs/api/_src/api/pipelines/sync.md
index 8cc02209da..da1f468fe5 100644
--- a/docs/api/_src/api/sync.md
+++ b/docs/api/_src/api/pipelines/sync.md
@@ -1,7 +1,7 @@
 # nf_core.sync
 
 ```{eval-rst}
-.. automodule:: nf_core.sync
+.. automodule:: nf_core.pipelines.sync
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/utils.md b/docs/api/_src/api/pipelines/utils.md
similarity index 74%
rename from docs/api/_src/api/utils.md
rename to docs/api/_src/api/pipelines/utils.md
index 1353f97ef5..86b8c3f36f 100644
--- a/docs/api/_src/api/utils.md
+++ b/docs/api/_src/api/pipelines/utils.md
@@ -1,7 +1,7 @@
 # nf_core.utils
 
 ```{eval-rst}
-.. automodule:: nf_core.utils
+.. automodule:: nf_core.pipelines.utils
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/api/_src/api/subworkflows.md b/docs/api/_src/api/subworkflows.md
deleted file mode 100644
index 438ccd0185..0000000000
--- a/docs/api/_src/api/subworkflows.md
+++ /dev/null
@@ -1,9 +0,0 @@
-# nf_core.subworkflows
-
-```{eval-rst}
-.. automodule:: nf_core.subworkflows
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :private-members:
-```
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
index 037ca95475..d81a0e90d4 100644
--- a/docs/api/_src/index.md
+++ b/docs/api/_src/index.md
@@ -1,22 +1,10 @@
 # nf-core/tools documentation
 
-```{toctree}
-:caption: 'Contents:'
-:glob: true
-:hidden: true
-:maxdepth: 2
-
-pipeline_lint_tests/index.rst
-module_lint_tests/index.rst
-subworkflow_lint_tests/index.rst
-api/index.rst
-```
-
-This documentation is for the `nf-core/tools` package.
+This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/tools) package.
 
 ## Contents
 
-- [Pipeline code lint tests](pipeline_lint_tests/index.md) (run by `nf-core pipelines lint`)
-- [Module code lint tests](module_lint_tests/index.md) (run by `nf-core modules lint`)
-- [Subworkflow code lint tests](subworkflow_lint_tests/index.md) (run by `nf-core subworkflows lint`)
-- [nf-core/tools Python package API reference](api/index.md)
+- [Pipeline code lint tests](./pipeline_lint_tests/) (run by `nf-core pipelines lint`)
+- [Module code lint tests](./module_lint_tests/) (run by `nf-core modules lint`)
+- [Subworkflow code lint tests](./subworkflow_lint_tests/) (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference](./api/)
diff --git a/docs/api/_src/module_lint_tests/index.md b/docs/api/_src/module_lint_tests/index.md
index dee84d06d8..7039ba2598 100644
--- a/docs/api/_src/module_lint_tests/index.md
+++ b/docs/api/_src/module_lint_tests/index.md
@@ -1,8 +1,11 @@
-# Module lint tests
+# Module Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [environment_yml](./environment_yml/)
+    - [main_nf](./main_nf/)
+    - [meta_yml](./meta_yml/)
+    - [module_changes](./module_changes/)
+    - [module_deprecations](./module_deprecations/)
+    - [module_patch](./module_patch/)
+    - [module_tests](./module_tests/)
+    - [module_todos](./module_todos/)
+    - [module_version](./module_version/)
diff --git a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
index c0f0aef5a4..4bb47569ac 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_awsfulltest.md
@@ -1,5 +1,5 @@
 # actions_awsfulltest
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_awsfulltest
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awsfulltest
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_awstest.md b/docs/api/_src/pipeline_lint_tests/actions_awstest.md
index 42441c8ac5..b250571a04 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_awstest.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_awstest.md
@@ -1,5 +1,5 @@
 # actions_awstest
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_awstest
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_awstest
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_ci.md b/docs/api/_src/pipeline_lint_tests/actions_ci.md
index 78ea3aea0d..68cbc089ad 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_ci.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_ci.md
@@ -1,5 +1,5 @@
 # actions_ci
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_ci
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_ci
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
index f0c98eb213..860acb2d2e 100644
--- a/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
+++ b/docs/api/_src/pipeline_lint_tests/actions_schema_validation.md
@@ -1,5 +1,5 @@
 # actions_schema_validation
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.actions_schema_validation
+.. automethod:: nf_core.pipelines.lint.PipelineLint.actions_schema_validation
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/base_config.md b/docs/api/_src/pipeline_lint_tests/base_config.md
index 4a56ef9789..803627ced0 100644
--- a/docs/api/_src/pipeline_lint_tests/base_config.md
+++ b/docs/api/_src/pipeline_lint_tests/base_config.md
@@ -1,5 +1,5 @@
 # base_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.base_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.base_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/files_exist.md b/docs/api/_src/pipeline_lint_tests/files_exist.md
index 309ea62f0b..69890d1690 100644
--- a/docs/api/_src/pipeline_lint_tests/files_exist.md
+++ b/docs/api/_src/pipeline_lint_tests/files_exist.md
@@ -1,5 +1,5 @@
 # files_exist
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.files_exist
+.. automethod:: nf_core.pipelines.lint.PipelineLint.files_exist
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/files_unchanged.md b/docs/api/_src/pipeline_lint_tests/files_unchanged.md
index 2f3b04fe1b..3f626e5b8d 100644
--- a/docs/api/_src/pipeline_lint_tests/files_unchanged.md
+++ b/docs/api/_src/pipeline_lint_tests/files_unchanged.md
@@ -1,5 +1,5 @@
 # files_unchanged
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.files_unchanged
+.. automethod:: nf_core.pipelines.lint.PipelineLint.files_unchanged
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md
index c631610d64..3575c08db4 100644
--- a/docs/api/_src/pipeline_lint_tests/index.md
+++ b/docs/api/_src/pipeline_lint_tests/index.md
@@ -1,8 +1,25 @@
-# Pipeline lint tests
+# Pipeline Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [actions_awsfulltest](./actions_awsfulltest/)
+    - [actions_awstest](./actions_awstest/)
+    - [actions_ci](./actions_ci/)
+    - [actions_schema_validation](./actions_schema_validation/)
+    - [base_config](./base_config/)
+    - [files_exist](./files_exist/)
+    - [files_unchanged](./files_unchanged/)
+    - [merge_markers](./merge_markers/)
+    - [modules_config](./modules_config/)
+    - [modules_json](./modules_json/)
+    - [modules_structure](./modules_structure/)
+    - [multiqc_config](./multiqc_config/)
+    - [nextflow_config](./nextflow_config/)
+    - [nfcore_yml](./nfcore_yml/)
+    - [pipeline_name_conventions](./pipeline_name_conventions/)
+    - [pipeline_todos](./pipeline_todos/)
+    - [readme](./readme/)
+    - [schema_description](./schema_description/)
+    - [schema_lint](./schema_lint/)
+    - [schema_params](./schema_params/)
+    - [system_exit](./system_exit/)
+    - [template_strings](./template_strings/)
+    - [version_consistency](./version_consistency/)
diff --git a/docs/api/_src/pipeline_lint_tests/merge_markers.md b/docs/api/_src/pipeline_lint_tests/merge_markers.md
index b52fdba1a8..7b620b4af1 100644
--- a/docs/api/_src/pipeline_lint_tests/merge_markers.md
+++ b/docs/api/_src/pipeline_lint_tests/merge_markers.md
@@ -1,5 +1,5 @@
 # merge_markers
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.merge_markers
+.. automethod:: nf_core.pipelines.lint.PipelineLint.merge_markers
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_config.md b/docs/api/_src/pipeline_lint_tests/modules_config.md
index 2a4f51c5a4..c8eac0cf9d 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_config.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_config.md
@@ -1,5 +1,5 @@
 # modules_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_json.md b/docs/api/_src/pipeline_lint_tests/modules_json.md
index 0c0ba71a8f..3070f83f57 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_json.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_json.md
@@ -1,5 +1,5 @@
-# nextflow_config
+# modules_json
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_json
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_json
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/modules_structure.md b/docs/api/_src/pipeline_lint_tests/modules_structure.md
index faa39ca77f..8a83918857 100644
--- a/docs/api/_src/pipeline_lint_tests/modules_structure.md
+++ b/docs/api/_src/pipeline_lint_tests/modules_structure.md
@@ -1,5 +1,5 @@
 # modules_structure
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.modules_structure
+.. automethod:: nf_core.pipelines.lint.PipelineLint.modules_structure
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/multiqc_config.md b/docs/api/_src/pipeline_lint_tests/multiqc_config.md
index 311f6b3049..281957749a 100644
--- a/docs/api/_src/pipeline_lint_tests/multiqc_config.md
+++ b/docs/api/_src/pipeline_lint_tests/multiqc_config.md
@@ -1,5 +1,5 @@
 # multiqc_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.multiqc_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.multiqc_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/nextflow_config.md b/docs/api/_src/pipeline_lint_tests/nextflow_config.md
index e23e966143..98e8df2574 100644
--- a/docs/api/_src/pipeline_lint_tests/nextflow_config.md
+++ b/docs/api/_src/pipeline_lint_tests/nextflow_config.md
@@ -1,5 +1,5 @@
 # nextflow_config
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.nextflow_config
+.. automethod:: nf_core.pipelines.lint.PipelineLint.nextflow_config
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
index f7e797a29c..226eb4c948 100644
--- a/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
+++ b/docs/api/_src/pipeline_lint_tests/nfcore_yml.md
@@ -1,5 +1,5 @@
 # nfcore_yml
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.nfcore_yml
+.. automethod:: nf_core.pipelines.lint.PipelineLint.nfcore_yml
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
index 0034319d3d..09396b6afd 100644
--- a/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
+++ b/docs/api/_src/pipeline_lint_tests/pipeline_name_conventions.md
@@ -1,5 +1,5 @@
 # pipeline_name_conventions
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.pipeline_name_conventions
+.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_name_conventions
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
index 08e456ea22..8292075b91 100644
--- a/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
+++ b/docs/api/_src/pipeline_lint_tests/pipeline_todos.md
@@ -1,5 +1,5 @@
 # pipeline_todos
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.pipeline_todos
+.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_todos
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/readme.md b/docs/api/_src/pipeline_lint_tests/readme.md
index 9583a56e0a..bf947bb61e 100644
--- a/docs/api/_src/pipeline_lint_tests/readme.md
+++ b/docs/api/_src/pipeline_lint_tests/readme.md
@@ -1,5 +1,5 @@
 # readme
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.readme
+.. automethod:: nf_core.pipelines.lint.PipelineLint.readme
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_description.md b/docs/api/_src/pipeline_lint_tests/schema_description.md
index 14f756acd2..0429b3cc10 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_description.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_description.md
@@ -1,5 +1,5 @@
 # schema_description
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_description
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_description
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_lint.md b/docs/api/_src/pipeline_lint_tests/schema_lint.md
index 39be2ea65c..95bd5cc2fc 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_lint.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_lint.md
@@ -1,5 +1,5 @@
 # schema_lint
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_lint
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_lint
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/schema_params.md b/docs/api/_src/pipeline_lint_tests/schema_params.md
index 80a626e880..8c6594c57b 100644
--- a/docs/api/_src/pipeline_lint_tests/schema_params.md
+++ b/docs/api/_src/pipeline_lint_tests/schema_params.md
@@ -1,5 +1,5 @@
 # schema_params
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.schema_params
+.. automethod:: nf_core.pipelines.lint.PipelineLint.schema_params
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/system_exit.md b/docs/api/_src/pipeline_lint_tests/system_exit.md
index 3d0ac20f8d..9ba67d4d2f 100644
--- a/docs/api/_src/pipeline_lint_tests/system_exit.md
+++ b/docs/api/_src/pipeline_lint_tests/system_exit.md
@@ -1,5 +1,5 @@
 # system_exit
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.system_exit
+.. automethod:: nf_core.pipelines.lint.PipelineLint.system_exit
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/template_strings.md b/docs/api/_src/pipeline_lint_tests/template_strings.md
index 3d03bfb256..ee334a2a21 100644
--- a/docs/api/_src/pipeline_lint_tests/template_strings.md
+++ b/docs/api/_src/pipeline_lint_tests/template_strings.md
@@ -1,5 +1,5 @@
 # template_strings
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.template_strings
+.. automethod:: nf_core.pipelines.lint.PipelineLint.template_strings
 ```
diff --git a/docs/api/_src/pipeline_lint_tests/version_consistency.md b/docs/api/_src/pipeline_lint_tests/version_consistency.md
index e8038f8531..868a348704 100644
--- a/docs/api/_src/pipeline_lint_tests/version_consistency.md
+++ b/docs/api/_src/pipeline_lint_tests/version_consistency.md
@@ -1,5 +1,5 @@
 # version_consistency
 
 ```{eval-rst}
-.. automethod:: nf_core.lint.PipelineLint.version_consistency
+.. automethod:: nf_core.pipelines.lint.PipelineLint.version_consistency
 ```
diff --git a/docs/api/_src/subworkflow_lint_tests/index.md b/docs/api/_src/subworkflow_lint_tests/index.md
index 0ecf590c0d..da8db49a7b 100644
--- a/docs/api/_src/subworkflow_lint_tests/index.md
+++ b/docs/api/_src/subworkflow_lint_tests/index.md
@@ -1,8 +1,8 @@
-# Subworkflow lint tests
+# Subworkflow Lint Tests
 
-```{toctree}
-:glob: true
-:maxdepth: 1
-
-*
-```
+    - [main_nf](./main_nf/)
+    - [meta_yml](./meta_yml/)
+    - [subworkflow_changes](./subworkflow_changes/)
+    - [subworkflow_tests](./subworkflow_tests/)
+    - [subworkflow_todos](./subworkflow_todos/)
+    - [subworkflow_version](./subworkflow_version/)
diff --git a/docs/api/make_lint_md.py b/docs/api/make_lint_md.py
index 48393094b3..432f0d16b6 100644
--- a/docs/api/make_lint_md.py
+++ b/docs/api/make_lint_md.py
@@ -1,53 +1,57 @@
 #!/usr/bin/env python
-
-import fnmatch
-import os
+from pathlib import Path
 
 import nf_core.modules.lint
 import nf_core.pipelines.lint
 import nf_core.subworkflows.lint
 
 
-def make_docs(docs_basedir, lint_tests, md_template):
-    # Get list of existing .md files
-    existing_docs = []
-    for fn in os.listdir(docs_basedir):
-        if fnmatch.fnmatch(fn, "*.md") and not fnmatch.fnmatch(fn, "index.md"):
-            existing_docs.append(os.path.join(docs_basedir, fn))
+def create_docs(docs_basedir, lint_tests, md_template):
+    docs_basedir.mkdir(parents=True, exist_ok=True)
+    existing_docs = list(docs_basedir.glob("*.md"))
+    existing_docs.remove(docs_basedir / "index.md")
 
     for test_name in lint_tests:
-        fn = os.path.join(docs_basedir, f"{test_name}.md")
-        if os.path.exists(fn):
+        fn = docs_basedir / f"{test_name}.md"
+        if fn.exists():
             existing_docs.remove(fn)
         else:
             with open(fn, "w") as fh:
                 fh.write(md_template.format(test_name))
 
     for fn in existing_docs:
-        os.remove(fn)
+        fn.unlink()
+
+
+def create_index_file(basedir, title):
+    index_file = basedir / "index.md"
+    with open(index_file, "w") as fh:
+        fh.write(f"# {title}\n\n")
+        for fn in sorted(basedir.glob("*.md")):
+            if fn.name != "index.md":
+                fh.write(f"    - [{fn.stem}](./{fn.stem}/)\n")
 
 
 # Create the pipeline docs
-pipeline_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "pipeline_lint_tests")
-make_docs(
-    pipeline_docs_basedir,
+pipeline_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "pipeline_lint_tests"
+create_docs(
+    pipeline_lint_docs_basedir,
     nf_core.pipelines.lint.PipelineLint._get_all_lint_tests(True),
     """# {0}
 
-```{{eval-rst}}
-.. automethod:: nf_core.pipelines.lint.PipelineLint.{0}
-```
-""",
+    ```{{eval-rst}}
+    .. automethod:: nf_core.pipelines.lint.PipelineLint.{0}
+    ```
+    """,
 )
+create_index_file(pipeline_lint_docs_basedir, "Pipeline Lint Tests")
 
-# Create the modules lint docs
-modules_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "module_lint_tests")
-make_docs(
-    modules_docs_basedir,
-    list(
-        set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union(
-            nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False)
-        )
+# Create the modules docs
+modules_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "module_lint_tests"
+create_docs(
+    modules_lint_docs_basedir,
+    set(nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=True)).union(
+        nf_core.modules.lint.ModuleLint.get_all_module_lint_tests(is_pipeline=False)
     ),
     """# {0}
 
@@ -56,15 +60,14 @@ def make_docs(docs_basedir, lint_tests, md_template):
 ```
 """,
 )
+create_index_file(modules_lint_docs_basedir, "Module Lint Tests")
 
-# Create the subworkflows lint docs
-subworkflows_docs_basedir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "_src", "subworkflow_lint_tests")
-make_docs(
-    subworkflows_docs_basedir,
-    list(
-        set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union(
-            nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False)
-        )
+# Create the subworkflow docs
+subworkflow_lint_docs_basedir = Path(__file__).resolve().parent / "_src" / "subworkflow_lint_tests"
+create_docs(
+    subworkflow_lint_docs_basedir,
+    set(nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=True)).union(
+        nf_core.subworkflows.lint.SubworkflowLint.get_all_subworkflow_lint_tests(is_pipeline=False)
     ),
     """# {0}
 
@@ -73,3 +76,4 @@ def make_docs(docs_basedir, lint_tests, md_template):
 ```
 """,
 )
+create_index_file(subworkflow_lint_docs_basedir, "Subworkflow Lint Tests")