Skip to content

Commit ca7c05a

Browse files
authored
Merge pull request #268 from nf-core/dev
Release v2.4.1
2 parents 61d1919 + 2d1bc86 commit ca7c05a

File tree

29 files changed

+363
-101
lines changed

29 files changed

+363
-101
lines changed

.devcontainer/devcontainer.json

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,7 @@
22
"name": "nfcore",
33
"image": "nfcore/gitpod:latest",
44
"remoteUser": "gitpod",
5+
"runArgs": ["--privileged"],
56

67
// Configure tool-specific properties.
78
"customizations": {

.github/CONTRIBUTING.md

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
99
However, don't be put off by this template - other more general issues and suggestions are welcome!
1010
Contributions to the code are even more welcome ;)
1111

12-
> 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)).
12+
:::info
13+
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)).
14+
:::
1315

1416
## Contribution workflow
1517

.github/workflows/ci.yml

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -35,6 +35,12 @@ jobs:
3535
"test,docker --aligner universc -stub",
3636
]
3737
steps:
38+
- name: Free some space
39+
run: |
40+
sudo rm -rf /usr/share/dotnet
41+
sudo rm -rf /opt/ghc
42+
sudo rm -rf "/usr/local/share/boost"
43+
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
3844
- name: Check out pipeline code
3945
uses: actions/checkout@v3
4046

.github/workflows/linting.yml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ jobs:
7878

7979
- uses: actions/setup-python@v4
8080
with:
81-
python-version: "3.8"
81+
python-version: "3.11"
8282
architecture: "x64"
8383

8484
- name: Install dependencies
Lines changed: 68 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,68 @@
1+
name: release-announcements
2+
# Automatic release toot and tweet anouncements
3+
on:
4+
release:
5+
types: [published]
6+
workflow_dispatch:
7+
8+
jobs:
9+
toot:
10+
runs-on: ubuntu-latest
11+
steps:
12+
- uses: rzr/fediverse-action@master
13+
with:
14+
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
15+
host: "mstdn.science" # custom host if not "mastodon.social" (default)
16+
# GitHub event payload
17+
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
18+
message: |
19+
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
20+
21+
Please see the changelog: ${{ github.event.release.html_url }}
22+
23+
send-tweet:
24+
runs-on: ubuntu-latest
25+
26+
steps:
27+
- uses: actions/setup-python@v4
28+
with:
29+
python-version: "3.10"
30+
- name: Install dependencies
31+
run: pip install tweepy==4.14.0
32+
- name: Send tweet
33+
shell: python
34+
run: |
35+
import os
36+
import tweepy
37+
38+
client = tweepy.Client(
39+
access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
40+
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
41+
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
42+
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
43+
)
44+
tweet = os.getenv("TWEET")
45+
client.create_tweet(text=tweet)
46+
env:
47+
TWEET: |
48+
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
49+
50+
Please see the changelog: ${{ github.event.release.html_url }}
51+
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
52+
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
53+
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
54+
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
55+
56+
bsky-post:
57+
runs-on: ubuntu-latest
58+
steps:
59+
- uses: zentered/bluesky-post-action@v0.0.2
60+
with:
61+
post: |
62+
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
63+
64+
Please see the changelog: ${{ github.event.release.html_url }}
65+
env:
66+
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
67+
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
68+
#

CHANGELOG.md

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,11 @@
33
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
44
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
55

6-
## [Unpublished Version / DEV]
6+
## v2.4.1 - 2023-09-28
7+
8+
- Fix whitelist logic for dropseq ([#267](https://github.com/nf-core/scrnaseq/pull/267))
9+
- Fix false-positive filename check in cellranger module ([#261](https://github.com/nf-core/scrnaseq/pull/261))
10+
- Template update to v2.10 ([#269](https://github.com/nf-core/scrnaseq/pull/269))
711

812
## v2.4.0 - 2023-08-16 Lime Platinum Crab
913

CITATIONS.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212

1313
- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
1414

15-
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
15+
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
1616
1717
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
1818

0 commit comments

Comments
 (0)