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Merge pull request #1113 from nf-core/dev
Dev -> Master for 3.13.0 release
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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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Devcontainer specs:
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- [DevContainer config](.devcontainer/devcontainer.json)
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- [Dockerfile](.devcontainer/Dockerfile)

‎.github/ISSUE_TEMPLATE/bug_report.yml

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attributes:
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label: System information
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description: |
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* Nextflow version _(eg. 22.10.1)_
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* Nextflow version _(eg. 23.04.0)_
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* Hardware _(eg. HPC, Desktop, Cloud)_
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* Executor _(eg. slurm, local, awsbatch)_
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* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

‎.github/workflows/ci.yml

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strategy:
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matrix:
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NXF_VER:
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- "22.10.1"
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- "23.04.0"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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salmon:
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name: Test Salmon with workflow parameters
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pseudo:
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name: Test Pseudoaligners with workflow parameters
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if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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parameters:
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- "--skip_qc"
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- "--skip_alignment --skip_pseudo_alignment"
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- "--salmon_index false --transcript_fasta false"
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- "--pseudo_aligner salmon --skip_qc"
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- "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
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- "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
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- "--pseudo_aligner kallisto --skip_qc"
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- "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
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- "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Run pipeline with Salmon and various parameters
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- name: Run pipeline with Salmon or Kallisto and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

‎.github/workflows/cloud_tests_full.yml

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compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
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profiles: test_full_aws,public_aws_ecr
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profiles: test_full_aws
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parameters: |
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{
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"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",

‎.github/workflows/cloud_tests_small.yml

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compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
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workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
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run_name: "aws_rnaseq_small"
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profiles: test,public_aws_ecr
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profiles: test
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parameters: |
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{
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"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"

‎.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

‎.github/workflows/release-announcments.yml

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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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#

‎.gitpod.yml

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image: nfcore/gitpod:latest
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tasks:
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- name: Update Nextflow and setup pre-commit
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command: |
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pre-commit install --install-hooks
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nextflow self-update
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vscode:
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extensions: # based on nf-core.nf-core-extensionpack

‎.nf-core.yml

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files_unchanged:
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- assets/email_template.html
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- assets/email_template.txt
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- lib/NfcoreSchema.groovy
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- lib/NfcoreTemplate.groovy
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- pyproject.toml
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multiqc_config: false

‎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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## [[3.13.0](https://github.com/nf-core/rnaseq/releases/tag/3.13.0)] - 2023-11-17
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### Credits
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Special thanks to the following for their contributions to the release:
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- [Adam Talbot](https://github.com/adamrtalbot)
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- [hmehlan](https://github.com/hmehlan)
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- [Jonathan Manning](https://github.com/pinin4fjords)
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- [Júlia Mir Pedrol](https://github.com/mirpedrol)
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- [Matthias Zepper](https://github.com/MatthiasZepper)
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- [Maxime Garcia](https://github.com/maxulysse)
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- [Steffen Möller](https://github.com/smoe)
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Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
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### Enhancements & fixes
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- [PR #1049](https://github.com/nf-core/rnaseq/pull/1049) - Display a warning when `--extra_star_align_args` are used with `--aligner star_rsem`
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- [PR #1051](https://github.com/nf-core/rnaseq/pull/1051) - Remove `public_aws_ecr` profile
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- [PR #1054](https://github.com/nf-core/rnaseq/pull/1054) - Template update to nf-core/tools v2.9
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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 use of `--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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- [PR #1106](https://github.com/nf-core/rnaseq/pull/1106) - Kallisto quantification
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- [PR #1107](https://github.com/nf-core/rnaseq/pull/1107) - Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage
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- [#976](https://github.com/nf-core/rnaseq/issues/976) - Add author and licenses for all custom scripts
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- [#1050](https://github.com/nf-core/rnaseq/issues/1050) - Provide custom prefix/suffix for summary files to avoid overwriting
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- [#1074](https://github.com/nf-core/rnaseq/issues/1074) - Enable quantification using StringTie AND a custom
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- [#1082](https://github.com/nf-core/rnaseq/issues/1082) - More informative error message for `filter_gtf_for_genes_in_genome.py`
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- [#1102](https://github.com/nf-core/rnaseq/issues/1102) - gene entries with empty transcript_id fields
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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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| `multiqc` | 1.14 | 1.17 |
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| `ucsc-bedgraphtobigwig` | 377 | 445 |
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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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### Modules / Subworkflows
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| Script | Old name | New name |
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| ------------------------ | ----------------- | --------------------------- |
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| `local/gtf_filter` | `GTF_GENE_FILTER` | `GTF_FILTER` |
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| `local/tx2gene` | `SALMON_TX2GENE` | `TX2GENE` |
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| `local/tximport` | `SALMON_TXIMPORT` | `TXIMPORT` |
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| `local/quantify_salmon` | `QUANTIFY_SALMON` | `QUANTIFY_PSEUDO_ALIGNMENT` |
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| `nf-core/kallisto_index` | | `KALLISTO_INDEX` |
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| `nf-core/kallisto_quant` | | `KALLISTO_QUANT` |
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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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### Credits
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### Enhancements & fixes
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- [[#1011](https://github.com/nf-core/rnaseq/issues/1011)] - FastQ files from UMI-tools not being passed to fastp
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- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
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- [[#1018](https://github.com/nf-core/rnaseq/issues/1018)] - Ability to skip both alignment and pseudoalignment to only run pre-processing QC steps.
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- [PR #1016](https://github.com/nf-core/rnaseq/pull/1016) - Updated pipeline template to [nf-core/tools 2.8](https://github.com/nf-core/tools/releases/tag/2.8)
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- [PR #1025](https://github.com/nf-core/fetchngs/pull/1025) - Add `public_aws_ecr.config` to source mulled containers when using `public.ecr.aws` Docker Biocontainer registry
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- [PR #1038](https://github.com/nf-core/rnaseq/pull/1038) - Updated error log for count values when supplying `--additional_fasta`
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- Added options to skip several steps
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- Skip trimming using `--skipTrimming`
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- Skip BiotypeQC using `--skipBiotypeQC`
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- Skip Alignment using `--skipAlignment` to only use pseudo-alignment using Salmon
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- Skip Alignment using `--skipAlignment` to only use pseudoalignment using Salmon
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### Documentation updates
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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].
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- [featureCounts](https://pubmed.ncbi.nlm.nih.gov/24227677/)
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> Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014 Apr 1;30(7):923-30. doi: 10.1093/bioinformatics/btt656. Epub 2013 Nov 13. PubMed PMID: 24227677.
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- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
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> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
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- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
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> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

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