Skip to content

Navigation Menu

Appearance settings

GitHub Copilot
Write better code with AI

GitHub Spark New
Build and deploy intelligent apps

GitHub Models New
Manage and compare prompts

GitHub Advanced Security
Find and fix vulnerabilities

Actions
Automate any workflow
Codespaces
Instant dev environments

Issues
Plan and track work

Code Review
Manage code changes

Discussions
Collaborate outside of code

Code Search
Find more, search less
Explore

Why GitHub

Documentation

GitHub Skills

Blog
Integrations

GitHub Marketplace

MCP Registry
View all features
By company size

Enterprises

Small and medium teams

Startups

Nonprofits
By use case

App Modernization

DevSecOps

DevOps

CI/CD

View all use cases
By industry

Healthcare

Financial services

Manufacturing

Government

View all industries
View all solutions
Topics

AI

DevOps

Security

Software Development

View all
Explore

Learning Pathways

Events & Webinars

Ebooks & Whitepapers

Customer Stories

Partners

Executive Insights
GitHub Sponsors
Fund open source developers
The ReadME Project
GitHub community articles
Repositories

Topics

Trending

Collections
Enterprise platform
AI-powered developer platform
Available add-ons

GitHub Advanced Security
Enterprise-grade security features

Copilot for business
Enterprise-grade AI features

Premium Support
Enterprise-grade 24/7 support
Pricing

Search code, repositories, users, issues, pull requests...

Search

Clear

Search syntax tips

Provide feedback

We read every piece of feedback, and take your input very seriously.

Include my email address so I can be contacted

Saved searches

Use saved searches to filter your results more quickly

Name

Query

To see all available qualifiers, see our documentation.

Appearance settings

You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. You switched accounts on another tab or window. Reload to refresh your session.

Dismiss alert

nf-core / tools Public

Notifications You must be signed in to change notification settings
Fork 214
Star 273

Code
Issues 314
Pull requests 33
Actions
Security
Insights

Additional navigation options

Code
Issues
Pull requests
Actions
Security
Insights

Enable parsing of multi-line config values#3629

Merged

MatthiasZepper merged 6 commits intonf-core:devnf-core/tools:devfrom

MatthiasZepper:pair_genome_alignMatthiasZepper/tools:pair_genome_alignCopy head branch name to clipboard

Jul 7, 2025

Conversation Commits6 (6)Checks Files changed

Merged

Enable parsing of multi-line config values#3629
MatthiasZepper merged 6 commits intonf-core:devfrom
MatthiasZepper:pair_genome_align

Commits

Commits on Jul 7, 2025

Add pairgenomealign config to test cases for nf-core pipelines download.
MatthiasZepper
committed
feat:download Eliminate known false positives also from direct matches.
MatthiasZepper
committed
feat:config_parser Enable parsing of multi-line config values with nextflow config --flat
MatthiasZepper
committed
[automated] Update CHANGELOG.md

nf-core-bot
authored and
MatthiasZepper
committed
Handle empty string config values: Change regex to avoid catastrophic backtracking and assign them to the dict as well.
MatthiasZepper
committed
Set config value to null for empty values like it is done for parameters parsed from main.nf
MatthiasZepper
committed

Footer

© 2025 GitHub, Inc.

Footer navigation

Terms
Privacy
Security
Status
Community
Docs
Contact

You can’t perform that action at this time.