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Template update for nf-core/tools version 2.10
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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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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v3.12.0 - [date]
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## v3.13.0dev - [date]
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Initial release of nf-core/rnaseq, created with the [nf-core](https://nf-co.re/) template.
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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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- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
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CODE_OF_CONDUCT.md

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README.md

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# ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_light.png#gh-light-mode-only) ![nf-core/rnaseq](docs/images/nf-core-rnaseq_logo_dark.png#gh-dark-mode-only)
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[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
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[![GitHub Actions CI Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+CI%22)
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[![GitHub Actions Linting Status](https://github.com/nf-core/rnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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## Usage
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> **Note**
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> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
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> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
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> with `-profile test` before running the workflow on actual data.
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:::note
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If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
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to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
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with `-profile test` before running the workflow on actual data.
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:::
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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
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Explain what rows and columns represent. For instance (please edit as appropriate):
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--outdir <OUTDIR>
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```
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> **Warning:**
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> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
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> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
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> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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:::warning
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Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
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provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
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see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
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:::
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For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/rnaseq/usage) and the [parameter documentation](https://nf-co.re/rnaseq/parameters).
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assets/multiqc_config.yml

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/rnaseq/3.12.0" target="_blank">nf-core/rnaseq</a>
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This report has been generated by the <a href="https://github.com/nf-core/rnaseq/releases/tag/dev" target="_blank">nf-core/rnaseq</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/rnaseq/3.12.0/output" target="_blank">documentation</a>.
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<a href="https://nf-co.re/rnaseq/dev/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-rnaseq-methods-description":
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order: -1000

conf/modules.config

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]
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}
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withName: 'MULTIQC' {
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ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
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publishDir = [
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path: { "${params.outdir}/multiqc" },
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mode: params.publish_dir_mode,
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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}

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