Merge pull request #3598 from mashehu/fix-api-docs-again

Author: mashehu

nf_core/pipelines/lint/nextflow_config.py

@@ -80,11 +80,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     * ``params.nf_required_version``: The old method for specifying the minimum Nextflow version. Replaced by ``manifest.nextflowVersion``
     * ``params.container``: The old method for specifying the dockerhub container address. Replaced by ``process.container``
     * ``igenomesIgnore``: Changed to ``igenomes_ignore``
-    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive in config files.
-    * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits`directive.
-    * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits`directive.
+    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits` directive in config files.
+    * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits` directive.
+    * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits` directive.
 
-        .. tip:: The ``snake_case`` convention should now be used when defining pipeline parameters
+    .. tip:: The ``snake_case`` convention should now be used when defining pipeline parameters
 
     **The following Nextflow syntax is depreciated and fails the test if present:**
 

nf_core/pipelines/lint/nf_test_content.py

@@ -55,13 +55,15 @@ def nf_test_content(self) -> Dict[str, List[str]]:
 
     All these checks can be skipped in the `.nf-core.yml` file using:
 
-        .. code-block:: groovy
+        .. code-block:: yaml
+
             lint:
                 nf_test_content: False
 
-        or
+    or
+
+        .. code-block:: yaml
 
-        .. code-block:: groovy
             lint:
                 nf_test_content:
                     - tests/<test_name>.nf.test

nf_core/pipelines/lint/nfcore_yml.py

@@ -15,11 +15,11 @@ def nfcore_yml(self) -> Dict[str, List[str]]:
 
     * repository type:
 
-        * Check that the repository type is set.
+        Check that the repository type is set.
 
     * nf core version:
 
-         * Check if the nf-core version is set to the latest version.
+        Check if the nf-core version is set to the latest version.
 
     """
     passed: List[str] = []

nf_core/pipelines/lint/readme.py

@@ -26,6 +26,7 @@ def readme(self):
     To disable this test, add the following to the pipeline's ``.nf-core.yml`` file:
 
     .. code-block:: yaml
+
         lint:
             readme: False
 

nf_core/pipelines/lint/schema_lint.py

@@ -20,7 +20,7 @@ def schema_lint(self):
     * Parameters can be described in two places:
 
         * As ``properties`` in the top-level schema object
-        * As ``properties`` within subschemas listed in a top-level ``definitions``(draft 7) or ``$defs``(draft 2020-12) objects
+        * As ``properties`` within subschemas listed in a top-level ``definitions`` (draft 7) or ``$defs`` (draft 2020-12) objects
 
     * The schema must describe at least one parameter
     * There must be no duplicate parameter IDs across the schema and definition subschema

nf_core/pipelines/lint/version_consistency.py

@@ -12,7 +12,7 @@ def version_consistency(self):
     * The pipeline config, ``manifest.version``
     * The docker container in the pipeline config, ``process.container``
 
-        * Some pipelines may not have this set on a pipeline level. If it is not found, it is ignored.
+        Some pipelines may not have this set on a pipeline level. If it is not found, it is ignored.
 
     * ``$GITHUB_REF``, if it looks like a release tag (``refs/tags/<something>``)