Merge pull request #3130 from mirpedrol/template-customisation-docume…

…ntation

Template: add option to exclude documentation from pipeline template

CHANGELOG.md

@@ -31,6 +31,7 @@
 - add option to exclude license from pipeline template ([#3125](https://github.com/nf-core/tools/pull/3125))
 - add option to exclude email from pipeline template ([#3126](https://github.com/nf-core/tools/pull/3126))
 - add option to exclude fastqc from pipeline template ([#3129](https://github.com/nf-core/tools/pull/3129))
+- add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130))
 
 ### Linting
 

nf_core/pipelines/create/templatefeatures.yml

@@ -310,3 +310,23 @@ slackreport:
       - ".prettierignore"
   nfcore_pipelines: False
   custom_pipelines: True
+documentation:
+  skippable_paths:
+    - "docs"
+  short_description: "Add documentation"
+  description: "Add documentation to the pipeline"
+  help_text: |
+    This will add documentation markdown files where you can describe your pipeline.
+    It includes:
+    - docs/README.md: A README file where you can describe the structure of your documentation.
+    - docs/output.md: A file where you can explain the output generated by the pipeline
+    - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters.
+
+    These files come with an exemplary documentation structure written.
+  linting:
+    files_exist:
+      - "docs/output.md"
+      - "docs/README.md"
+      - "docs/usage.md"
+  nfcore_pipelines: False
+  custom_pipelines: True