Merge pull request #1491 from nf-core/dev

v2.3.2 release

CHANGELOG.md

@@ -1,5 +1,16 @@
 # nf-core/tools: Changelog
 
+## [v2.3.2 - Mercury Vulture Fixed Formatting](https://github.com/nf-core/tools/releases/tag/2.3.2) - [2022-03-24]
+
+Very minor patch release to fix the full size AWS tests and re-run the template sync, which partially failed due to GitHub pull-requests being down at the time of release.
+
+### Template
+
+- Updated the AWS GitHub actions to let nf-core/tower-action use it's defaults for pipeline and git sha ([#1488](https://github.com/nf-core/tools/pull/1488))
+- Add prettier editor extension to `gitpod.yml` in template ([#1485](https://github.com/nf-core/tools/pull/1485))
+- Remove traces of markdownlint in the template ([#1486](https://github.com/nf-core/tools/pull/1486)
+- Remove accidentally added line in `CHANGELOG.md` in the template ([#1487](https://github.com/nf-core/tools/pull/1487))
+
 ## [v2.3.1 - Mercury Vulture Formatting](https://github.com/nf-core/tools/releases/tag/2.3.1) - [2022-03-23]
 
 This patch release is primarily to address problems that we had in the v2.3 release with code linting.
@@ -44,8 +55,6 @@ Please note that there are many excellent integrations for Prettier available, f
 - New pipeline lint test `multiqc_config` that checks YAML structure instead of basic file contents ([#1461](https://github.com/nf-core/tools/pull/1461))
 - Updates to the GitPod docker image to install the latest version of nf-core/tools
 
-### Modules
-
 ## [v2.3 - Mercury Vulture](https://github.com/nf-core/tools/releases/tag/2.3) - [2022-03-15]
 
 ### Template

nf_core/lint/files_exist.py

@@ -82,6 +82,7 @@ def files_exist(self):
         .github/ISSUE_TEMPLATE/feature_request.md
         docs/images/nf-core-PIPELINE_logo.png
         .markdownlint.yml
+        .yamllint.yml
 
     Files that *should not* be present:
 
@@ -164,6 +165,7 @@ def files_exist(self):
         os.path.join(".github", "ISSUE_TEMPLATE", "feature_request.md"),
         os.path.join("docs", "images", f"nf-core-{short_name}_logo.png"),
         ".markdownlint.yml",
+        ".yamllint.yml",
     ]
     files_warn_ifexists = [".travis.yml"]
 

nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md

@@ -10,7 +10,6 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/tree/master/.github/CONTRIBUTING.md)
 -->
-<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 

nf_core/pipeline-template/.github/workflows/awsfulltest.yml

@@ -22,8 +22,6 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
-          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {

nf_core/pipeline-template/.github/workflows/awstest.yml

@@ -17,8 +17,6 @@ jobs:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
-          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}{% endraw %}/work/{{ short_name }}/{% raw %}work-${{ github.sha }}{% endraw %}
           parameters: |
             {

nf_core/pipeline-template/.gitpod.yml

@@ -4,7 +4,7 @@ vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files
     # - cssho.vscode-svgviewer                 # SVG viewer
-    - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
     - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
     - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
     - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar

nf_core/pipeline-template/CHANGELOG.md

@@ -11,8 +11,6 @@ Initial release of {{ name }}, created with the [nf-core](https://nf-co.re/) tem
 
 ### `Fixed`
 
-- Clarified conda usage and added an installation tutorial for Singularity since the one on Syllabs' website uses an outdate version of GO Compiler
-
 ### `Dependencies`
 
 ### `Deprecated`

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import setup, find_packages
 
-version = "2.3.1"
+version = "2.3.2"
 
 with open("README.md") as f:
     readme = f.read()