Tutorial contributing to nf-core

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Phil Ewels, Gisela Gabernet, Rike Hanssen
Contributing to nf-core
Last updated March 2022

Documentation
Slack workspace
Hackathons
Twitter updates
Starter template
Code guidelines
Helper tools
CI code linting
and...

Contribution guidelines
Cooperate, don’t duplicate
One pipeline per analysis type, contribute
by adding new tools, new fea...

https://nf-co.re/usage/tutorials/nf_core_contributing_overview
2 Creating
3 Testing
4 Modules
5 Releasing
1 Installation
T...

Installation

Helper tools
pip install nf-core
conda install -c bioconda nf-core

Helper tools
nf-core --help

Helper tools
nf-core list

Creating pipelines 01
0110
0001
01101

nf-core create

Template
nf-core create

Template

Template

Template
├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── email_template.html
│ ...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── CHANGELOG.md
├── CITATIONS.md
├── CODE_OF_CONDUCT.md
├── LICENSE
├── README.md
├── assets
│ ├── ...
├── bin
│ └── ...
...

├── .editorconfig
├── .github
│ ├── .dockstore.yml
│ ├── CONTRIBUTING.md
│ ├── ISSUE_TEMPLATE
│ │ ├── bug_report.yml
│ │ ├...

Forks & branches

Forks & branches
Branch Merge

Forks & branches
@ewels
@nf-core
Fork

Forks & branches
Pull Request
Merge

dev
master
TEMPLATE
Forks & branches

dev
master
TEMPLATE
Forks & branches
Stable releases only

dev
master
TEMPLATE
Forks & branches
Used by @nf-core-bot
to keep in sync

dev
master
TEMPLATE
Forks & branches
All development code
(and all pull requests)

Forks & branches
PRs must be against the dev branch
Changelog must be updated
PRs need to be reviewed
REMEMBER!

Testing pipelines

Lint tests
nf-core lint

Lint tests
nf-core lint .
https://nf-co.re/errors

Test data
Make a new branch for your pipeline
Add a really (really!) tiny dataset
Set up the test config to use raw URLs

Exercises 2, 3
Exercise 2 (creating pipelines)
• Make a new pipeline using the template
• Update the readme file to fill i...

nf-core modules

modules
nf-core modules --help

modules
nf-core modules list

modules

modules
nf-core modules install

modules
nf-core modules create

Exercise 4
Exercise 4 (modules)
• Use the pipeline you created in Exercise 2 and add an
already existing nf-core module (e...

Releasing pipelines

First release
https://nf-co.re/developers/adding_pipelines
Tell us about it: #new-pipelines
Join the @nf-core organisation...

First release
https://nf-co.re/developers/adding_pipelines
Community review: "Pseudo PR"
Open PR from dev to master
Make s...

Version numbers
Semantic versioning: 1.4.3
Major - results not backwards compatible
Minor - new feature(s)
Patch - bug fix...

Help!
https://nf-co.re/join

Template updates

Exercise 5
Exercise 5 (releasing pipelines)
• Use nf-core bump-version to update the required version of Nextflow in your ...

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