nf-core · mashehu · Jun 2, 2025 · Jun 2, 2025 · Jun 2, 2025 · mirpedrol
diff --git a/docs/api/_src/index.md b/docs/api/_src/index.md
@@ -4,7 +4,7 @@ This API documentation is for the [`nf-core/tools`](https://github.com/nf-core/t
 
 ## Contents
 
-- [Pipeline code lint tests](./pipeline_lint_tests.md) (run by `nf-core pipelines lint`)
-- [Module code lint tests](./module_lint_tests.md) (run by `nf-core modules lint`)
-- [Subworkflow code lint tests](./subworkflow_lint_tests.md) (run by `nf-core subworkflows lint`)
-- [nf-core/tools Python package API reference](./api/index.md)
+- [Pipeline code lint tests](./pipeline_lint_tests/actions_awsfulltest.md) (run by `nf-core pipelines lint`)
+- [Module code lint tests](./module_lint_tests/environment_yml.md) (run by `nf-core modules lint`)
+- [Subworkflow code lint tests](./subworkflow_lint_tests/main_nf.md) (run by `nf-core subworkflows lint`)
+- [nf-core/tools Python package API reference](./api/utils.md)
diff --git a/nf_core/pipelines/lint/nf_test_content.py b/nf_core/pipelines/lint/nf_test_content.py
@@ -13,62 +13,67 @@ def nf_test_content(self) -> Dict[str, List[str]]:
 
     This lint test checks the following files and content of these files:
 
-    * `*.nf.test` files should specify the `outdir` parameter:
+    * ``*.nf.test`` files should specify the ``outdir`` parameter:
 
-        .. code-block:: groovy
+    .. code-block:: groovy
 
-            when {
-                params {
-                    outdir = "$outputDir"
-                }
+        when {
+            params {
+                outdir = "$outputDir"
             }
+        }
 
     * A `versions.yml` file should be included in the snapshot of all `*.nf.test` files
 
     * The `nextflow.config` file should contain:
+
         .. code-block:: groovy
+
             modules_testdata_base_path = <path>
 
+        and
+
         .. code-block:: groovy
+
             pipelines_testdata_base_path = <path>
 
         And should set the correct resource limits, as defined in the `test` profile
 
     * The `nf-test.config` file should:
         * Make sure tests are relative to root directory
 
-            .. code-block:: groovy
+        .. code-block:: groovy
 
-                testsDir "."
+            testsDir "."
 
         * Ensure a user-configurable nf-test directory
 
-            .. code-block:: groovy
+        .. code-block:: groovy
 
-                workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
+            workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
         * Use a test specific config
 
-            .. code-block:: groovy
+        .. code-block:: groovy
 
-                configFile "tests/nextflow.config"
+            configFile "tests/nextflow.config"
 
     All these checks can be skipped in the `.nf-core.yml` file using:
 
-        .. code-block:: yaml
+    .. code-block:: yaml
 
-            lint:
-                nf_test_content: False
+        lint:
+            nf_test_content: False
 
     or
 
-        .. code-block:: yaml
+    .. code-block:: yaml
 
-            lint:
-                nf_test_content:
-                    - tests/<test_name>.nf.test
-                    - tests/nextflow.config
-                    - nf-test.config
+        lint:
+            nf_test_content:
+                - tests/<test_name>.nf.test
+                - tests/nextflow.config
+                - nf-test.config
     """
     passed: List[str] = []
     failed: List[str] = []