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.devcontainer/devcontainer.json

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

.github/CONTRIBUTING.md

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

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- uses: actions/setup-python@v4
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with:
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python-version: "3.8"
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python-version: "3.11"
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architecture: "x64"
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- name: Install dependencies
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name: release-announcements
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# Automatic release toot and tweet anouncements
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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toot:
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runs-on: ubuntu-latest
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steps:
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- uses: rzr/fediverse-action@master
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with:
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access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
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host: "mstdn.science" # custom host if not "mastodon.social" (default)
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# GitHub event payload
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# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
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message: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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send-tweet:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: pip install tweepy==4.14.0
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- name: Send tweet
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shell: python
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run: |
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import os
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import tweepy
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client = tweepy.Client(
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access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
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access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
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consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
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consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
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)
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tweet = os.getenv("TWEET")
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client.create_tweet(text=tweet)
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env:
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TWEET: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
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TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
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TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
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TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
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bsky-post:
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runs-on: ubuntu-latest
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steps:
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- uses: zentered/[email protected]
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with:
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post: |
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Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
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Please see the changelog: ${{ github.event.release.html_url }}
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env:
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BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
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BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
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#

CHANGELOG.md

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- [PR #1058](https://github.com/nf-core/rnaseq/pull/1058) - Use `nf-validation` plugin for parameter and samplesheet validation
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- [PR #1068](https://github.com/nf-core/rnaseq/pull/1068) - Update `grep` version for `untar` module
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- [PR #1073](https://github.com/nf-core/rnaseq/pull/1073) - Update documentation to discourage --genome
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- [PR #1078](https://github.com/nf-core/rnaseq/pull/1078) - Updated pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10)
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- [PR #1083](https://github.com/nf-core/rnaseq/pull/1083) - Move local modules and subworkflows to subfolders
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- [PR #1088](https://github.com/nf-core/rnaseq/pull/1088) - Updates contributing and code of conduct documents with nf-core template 2.10
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- [PR #1091](https://github.com/nf-core/rnaseq/pull/1091) - Reorganise parameters in schema for better usability
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### Software dependencies
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| Dependency | Old version | New version |
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| ---------- | ----------- | ----------- |
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| `fastqc` | 0.11.9 | 0.12.1 |
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> **NB:** Dependency has been **updated** if both old and new version information is present.
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>
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> **NB:** Dependency has been **added** if just the new version information is present.
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>
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> **NB:** Dependency has been **removed** if new version information isn't present.
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## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02
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CITATIONS.md

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- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
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> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
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- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
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