Merge branch 'dev' into fix-modules-list-json

.github/workflows/create-lint-wf.yml

@@ -93,7 +93,7 @@ jobs:
 
       # Run nf-core linting
       - name: nf-core lint
-        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
+        run: nf-core --verbose --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned
         working-directory: create-lint-wf
 
       # Run the other nf-core commands

CHANGELOG.md

@@ -10,12 +10,15 @@
 - switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
 - Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 - Fix tyop in pipeline nextflow.config ([#2664](https://github.com/nf-core/tools/pull/2664))
+- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
 
 ### Download
 
 ### Linting
 
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
+- linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
+- environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
 
 ### Modules
 
@@ -34,7 +37,9 @@
 - Fix Renovate Dockerfile updating issues ([#2648](https://github.com/nf-core/tools/pull/2648) and [#2651](https://github.com/nf-core/tools/pull/2651))
 - Add new subcommand `nf-core tui`, which launches a TUI (terminal user interface) to intuitively explore the command line flags, built using [Trogon](https://github.com/Textualize/trogon) ([#2655](https://github.com/nf-core/tools/pull/2655))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.13 ([#2660](https://github.com/nf-core/tools/pull/2660))
+- Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([#2662](https://github.com/nf-core/tools/pull/2662))
 - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666))
+- Remove redundanct v in pipeline version for emails ([#2667](https://github.com/nf-core/tools/pull/2667))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 

MANIFEST.in

@@ -5,3 +5,7 @@ graft nf_core/pipeline-template
 graft nf_core/subworkflow-template
 include requirements.txt
 include nf_core/.pre-commit-prettier-config.yaml
+include nf_core/assets/logo/nf-core-repo-logo-base-lightbg.png
+include nf_core/assets/logo/nf-core-repo-logo-base-darkbg.png
+include nf_core/assets/logo/placeholder_logo.svg
+include nf_core/assets/logo/MavenPro-Bold.ttf