Merge pull request #2811 from nf-core/dev

Dev -> Master for 2.13.1

.devcontainer/devcontainer.json

@@ -11,15 +11,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.github/RELEASE_CHECKLIST.md

@@ -3,7 +3,7 @@
 1. Check issue milestones to see outstanding issues to resolve if possible or transfer to the milestones for the next release e.g. [`v1.9`](https://github.com/nf-core/tools/issues?q=is%3Aopen+is%3Aissue+milestone%3A1.9)
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
-4. Check that modules/subworkflows in tempalte are up to date with the latest releases
+4. Check that modules/subworkflows in template are up to date with the latest releases
 5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `setup.py` and change the gitpod container to `nfcore/gitpod:latest`.
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `master`

.github/actions/create-lint-wf/action.yml

@@ -17,7 +17,7 @@ runs:
 
     # Set up Nextflow
     - name: Install Nextflow
-      uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+      uses: nf-core/setup-nextflow@v1
       with:
         version: ${{ matrix.NXF_VER }}
 

.github/workflows/changelog.yml

@@ -4,6 +4,8 @@ on:
     types: [created]
   pull_request_target:
     types: [opened]
+    branches:
+      - dev
 
 jobs:
   update_changelog:

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

@@ -72,7 +72,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
         with:
           version: latest-everything
 

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

@@ -59,7 +59,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
         with:
           version: ${{ matrix.NXF_VER }}
 

.github/workflows/pytest.yml

@@ -108,12 +108,18 @@ jobs:
           sudo add-apt-repository --remove ppa:git-core/ppa
           sudo apt install -y git
 
+      - name: Set up Singularity
+        if: ${{ matrix.test == 'test_download.py'}}
+        uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
+        with:
+          singularity-version: 3.8.3
+
       - name: Get current date
         id: date
         run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - name: Look if nf-test is already installed and write to env variable
         id: check-nftest
@@ -191,14 +197,14 @@ jobs:
           mv .github/.coveragerc .
 
       - name: Download all artifacts
-        uses: actions/download-artifact@eaceaf801fd36c7dee90939fad912460b18a1ffe # v4
+        uses: actions/download-artifact@87c55149d96e628cc2ef7e6fc2aab372015aec85 # v4
       - name: Run coverage
         run: |
           coverage combine --keep coverage*/.coverage*
           coverage report
           coverage xml
 
-      - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # v4
+      - uses: codecov/codecov-action@54bcd8715eee62d40e33596ef5e8f0f48dbbccab # v4
         with:
           files: coverage.xml
         env:

.github/workflows/rich-codex.yml

@@ -15,7 +15,7 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
 
       - name: Cache nf-test installation
         id: cache-software

.github/workflows/sync.yml

@@ -67,7 +67,7 @@ jobs:
           pip install .
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        uses: nf-core/setup-nextflow@v1
         with:
           version: "latest-everything"
 

.gitpod.yml

@@ -12,10 +12,7 @@ tasks:
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
-    - codezombiech.gitignore # Language support for .gitignore files
-    # - cssho.vscode-svgviewer               # SVG viewer
     - 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
     - mechatroner.rainbow-csv # Highlight columns in csv files in different colors

CHANGELOG.md

@@ -1,5 +1,28 @@
 # nf-core/tools: Changelog
 
+## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]
+
+### Template
+
+- Remove obsolete editor settings in `devcontainer.json` and `gitpod.yml` ([#2795](https://github.com/nf-core/tools/pull/2795))
+- Add nf-test test instructions to contributing and PR template ([#2807](https://github.com/nf-core/tools/pull/2807))
+- Fix topic extraction step for hashtags in toots ([#2810](https://github.com/nf-core/tools/pull/2810))
+- Update modules and subworkflows in the template ([#2811](https://github.com/nf-core/tools/pull/2811))
+- Unpin setup-nextflow and action-tower-launch ([#2806](https://github.com/nf-core/tools/pull/2806))
+
+### Download
+
+- Improved offline container image resolution by introducing symlinks, fixes issues [#2751](https://github.com/nf-core/tools/issues/2751), [#2644](https://github.com/nf-core/tools/issues/2644) and [demultiplex#164](https://github.com/nf-core/demultiplex/issues/164): ([#2768](https://github.com/nf-core/tools/pull/2768))
+
+### Linting
+
+### Components
+
+### General
+
+- chore(deps): update codecov/codecov-action digest to 0cfda1d ([#2794](https://github.com/nf-core/tools/pull/2794))
+- chore(deps): update gitpod/workspace-base docker digest to c15ee2f ([#2799](https://github.com/nf-core/tools/pull/2799))
+
 ## [v2.13 - Tin Puppy](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-20]
 
 ### Template