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Merge pull request #524 from nf-core/dev
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Release: 2.5.0
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jfy133 authored Oct 10, 2023
2 parents 18a1645 + e219e7a commit ba72349
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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4 changes: 3 additions & 1 deletion .github/CONTRIBUTING.md
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Expand Up @@ -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/mag then the best place to ask is on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/mag then the best place to ask is on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

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2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
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Expand Up @@ -78,7 +78,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "3.8"
python-version: "3.11"
architecture: "x64"

- name: Install dependencies
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68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
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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/[email protected]
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 }}
#
27 changes: 26 additions & 1 deletion CHANGELOG.md
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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).

## 2.4.0 - 2023-09-25
## 2.5.0 - [2023-10-10]

### `Added`

- [#504](https://github.com/nf-core/mag/pull/504) - New parameters `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).

### `Changed`

- [#511](https://github.com/nf-core/mag/pull/511) - Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
- [#504](https://github.com/nf-core/mag/pull/504) - `--save_busco_reference` is now replaced by `--save_busco_db` (by @gregorysprenger).

### `Fixed`

- [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
- [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
- [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
- [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133)
- [#522](https://github.com/nf-core/mag/pull/522) - Fix 'nulls' in depth plot PNG files (fix by @jfy133)

### `Dependencies`

### `Deprecated`

- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_reference`, `--busco_download_path`, `--save_busco_reference` parameters have been deprecated and replaced with new parameters (by @gregorysprenger).

## 2.4.0 - 2023-09-26

### `Added`

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2 changes: 1 addition & 1 deletion CITATIONS.md
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- [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].
- [Filtlong](https://github.com/rrwick/Filtlong)

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