Merge pull request #3169 from mirpedrol/citationsmd

exclude CITATIONS.md file when excluding citations from pipeline template

CHANGELOG.md

@@ -23,7 +23,7 @@
 - Remove release announcement for non nf-core pipelines ([#3072](https://github.com/nf-core/tools/pull/3072))
 - handle template features with a yaml file ([#3108](https://github.com/nf-core/tools/pull/3108), [#3112](https://github.com/nf-core/tools/pull/3112))
 - add option to exclude code linters for custom pipeline template ([#3084](https://github.com/nf-core/tools/pull/3084))
-- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101))
+- add option to exclude citations for custom pipeline template ([#3101](https://github.com/nf-core/tools/pull/3101) and [#3169](https://github.com/nf-core/tools/pull/3169))
 - add option to exclude gitpod for custom pipeline template ([#3100](https://github.com/nf-core/tools/pull/3100))
 - add option to exclude codespaces from pipeline template ([#3105](https://github.com/nf-core/tools/pull/3105))
 - add option to exclude multiqc from pipeline template ([#3103](https://github.com/nf-core/tools/pull/3103))

nf_core/pipelines/create/template_features.yml

@@ -186,13 +186,17 @@ code_linters:
 citations:
   skippable_paths:
     - "assets/methods_description_template.yml"
+    - "CITATIONS.md"
   short_description: "Include citations"
   description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)."
   help_text: |
     If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline.
 
     Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline,
     and the logics to add this section to the output MultiQC report (if the report is generated).
+  linting:
+    files_exist:
+      - "CITATIONS.md"
   nfcore_pipelines: False
   custom_pipelines: True
 gitpod: