nf-core/viralrecon updates

Edit

This project aims to update nf-core/viralrecon pipeline by addressing key issues from the nf-core/viralrecon Hackathon March 2026 Milestone

Goal

1. Improve Nanopore data analysis for better long-read handling
   1. Add de novo assembly
   2. Add mapping, variant calling, and consensus genome generation independent of the ARTIC pipeline
2. Add IRMA (CDC) to viralrecon for RSV and influenza analysis
3. Improve the viralrecon de novo assembly subworkflow
4. Fix existing bugs

Milestone for the hackathon

Prior training

📚 We encourage participants to have completed the following Nextflow training materials:

• Hello nextflow
• Nextflow run
• Hello nf-core

Where

🌍 This project will be hybrid, online and in person, since contributors from outside Madrid are welcome.

📍 In Madrid, the project will take place at:

🇪🇸 ISCIII - Majadahonda Campus Building 53, Meeting Rooms 1 and 2 (To be confirmed)

We will have space for around 12 people.