Merge pull request #268 from nf-core/dev

Release v2.4.1

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
  "name": "nfcore",
  "image": "nfcore/gitpod:latest",
  "remoteUser": "gitpod",
+ "runArgs": ["--privileged"],
 
  // Configure tool-specific properties.
  "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 

.github/workflows/ci.yml

@@ -35,6 +35,12 @@ jobs:
  "test,docker --aligner universc -stub",
  ]
  steps:
+ - name: Free some space
+ run: |
+ sudo rm -rf /usr/share/dotnet
+ sudo rm -rf /opt/ghc
+ sudo rm -rf "/usr/local/share/boost"
+ sudo rm -rf "$AGENT_TOOLSDIRECTORY"
  - name: Check out pipeline code
  uses: actions/checkout@v3
 

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
  - uses: actions/setup-python@v4
  with:
- python-version: "3.8"
+ python-version: "3.11"
  architecture: "x64"
 
  - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+ release:
+ types: [published]
+ workflow_dispatch:
+
+jobs:
+ toot:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: rzr/fediverse-action@master
+ with:
+ access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+ host: "mstdn.science" # custom host if not "mastodon.social" (default)
+ # GitHub event payload
+ # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+ message: |
+ Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+ Please see the changelog: ${{ github.event.release.html_url }}
+
+ send-tweet:
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/setup-python@v4
+ with:
+ python-version: "3.10"
+ - name: Install dependencies
+ run: pip install tweepy==4.14.0
+ - name: Send tweet
+ shell: python
+ run: |
+ import os
+ import tweepy
+
+ client = tweepy.Client(
+ access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+ access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+ consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+ consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+ )
+ tweet = os.getenv("TWEET")
+ client.create_tweet(text=tweet)
+ env:
+ TWEET: |
+ Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+ Please see the changelog: ${{ github.event.release.html_url }}
+ TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+ TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+ TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+ TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+ bsky-post:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: zentered/bluesky-post-action@v0.0.2
+ with:
+ post: |
+ Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+ Please see the changelog: ${{ github.event.release.html_url }}
+ env:
+ BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+ BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+ #

CHANGELOG.md

@@ -3,7 +3,11 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unpublished Version / DEV]
+## v2.4.1 - 2023-09-28
+
+- Fix whitelist logic for dropseq ([#267](https://github.com/nf-core/scrnaseq/pull/267))
+- Fix false-positive filename check in cellranger module ([#261](https://github.com/nf-core/scrnaseq/pull/261))
+- Template update to v2.10 ([#269](https://github.com/nf-core/scrnaseq/pull/269))
 
 ## v2.4.0 - 2023-08-16 Lime Platinum Crab
 

CITATIONS.md

@@ -12,7 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
- > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+ > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)