Describe the bug
See https://github.com/grbot/chipimputation/tree/main/assets
Register with github apps, we saw that assets was missing although it should be a known directory according to https://nf-co.re/docs/contributing/pipelines/pipeline_file_structure

We were were able to workaround using https://github.com/dockstore/dockstore/pull/6165/files#diff-92ca178dc929d7e8d7e46033cb03fca4389361998f3b0f43f427113148bc9e4f to add the directories /assets and /templates

Expected behavior
/assets should be included by default

┆Issue is synchronized with this Jira Story
┆Issue Number: DOCK-2627
┆Sprint: 176 - Ysyk-Kol
┆Issue Type: Story