Issues

• FREYJA_BOOT intermittently fails: freyja boot bootstrap crashes when fracDefining rounds just above 1.0

  nf-core/viralrecon#618 · Filter by author pditommaso opened on Sep 4, 2026
  1

• Update pipeline nftests

  enhancement
  nf-core/viralrecon#616 · Filter by author LilyAnderssonLee opened on Aug 31, 2026 · 3.1
  

• Update primer file in genomes config

  enhancement
  nf-core/viralrecon#614 · Filter by author svarona opened on Aug 14, 2026 · 3.1

• Pipeline crashes on some samples with "invalid literal for int()" error, then a different error about DP field after workaround

  bug
  nf-core/viralrecon#604 · Filter by author mdhfz89 opened on Jul 8, 2026 · 3.1
  1

• Add primer trimming after assembly for enterovirus typing

  enhancement
  nf-core/viralrecon#603 · Filter by author AnnaNoren opened on Jul 3, 2026
  2

  

• Allow nanopore to have .fastq files in the samplesheet

  enhancement
  nf-core/viralrecon#600 · Filter by author svarona opened on May 26, 2026 · 3.1

• Min Quality differes between iVar and mpileup

  buggood first issue
  nf-core/viralrecon#598 · Filter by author svarona opened on May 18, 2026 · 3.1

• Allele mismatch in bcftools step

  bug
  nf-core/viralrecon#597 · Filter by author averagehat opened on May 13, 2026
  3

• Improve artic model selection

  bug
  nf-core/viralrecon#582 · Filter by author victor5lm opened on Mar 11, 2026 · 3.1
  1

• Add de novo assembler for nanopore data

  enhancement
  Enhancement

  nf-core/viralrecon#573 · Filter by author svarona opened on Nov 25, 2025 · 3.1
  

• Title: Support for Using Viralrecon with Other Arboviruses (e.g., Chikungunya and Dengue)

  question
  nf-core/viralrecon#570 · Filter by author nascimento-jean opened on Nov 20, 2025
  1

• Unable to run viralrecon using custom FASTA, GFF and Primer BED file for nanopore data

  bug
  nf-core/viralrecon#568 · Filter by author Rohit-Satyam opened on Nov 19, 2025

• Remove mandatory reference in de novo assembly

  nf-core/viralrecon#567 · Filter by author AnnaNoren opened on Nov 13, 2025 · Hackathon - March 2026
  

• Add filtering step of blast results

  nf-core/viralrecon#566 · Filter by author AnnaNoren opened on Nov 13, 2025 · 3.1
  

• Add documentation

  nf-core/viralrecon#565 · Filter by author AnnaNoren opened on Nov 13, 2025 · 3.1
  

• Add enterovirus testing profile

  nf-core/viralrecon#564 · Filter by author AnnaNoren opened on Nov 13, 2025 · 3.1
  

• Add ViralConsensus

  enhancement
  nf-core/viralrecon#561 · Filter by author niemasd opened on Nov 6, 2025

• fix release-announcements.yml

  bug
  nf-core/viralrecon#560 · Filter by author svarona opened on Nov 6, 2025 · 3.1

• BCFTools not running, but pipeline completing

  bug
  nf-core/viralrecon#557 · Filter by author fmtwohig opened on Oct 30, 2025

• Add enterovirus typing steps in de novo assembly

  documentationenhancementfeature-request
  Enhancement

  nf-core/viralrecon#555 · Filter by author AnnaNoren opened on Oct 29, 2025 · 3.1
  

• Work in PriorCons subworkflow integration at nf-core hackathon

  enhancement
  Enhancement

  nf-core/viralrecon#544 · Filter by author GERMAN00VP opened on Oct 28, 2025
  

• Allow to use pod5 instead of fast5

  enhancement
  Enhancement

  nf-core/viralrecon#543 · Filter by author svarona opened on Oct 28, 2025 · Hackathon - March 2026

• False “pycoqc” sample appears in MultiQC summary when no Nanopore samples pass filtering thresholds

  bug
  Bug

  nf-core/viralrecon#530 · Filter by author svarona opened on Oct 16, 2025 · Hackathon - March 2026
  

• Multi-batch data analysis with different library preparation methods

  question
  nf-core/viralrecon#529 · Filter by author YangJingqii opened on Oct 15, 2025

• Poor de novo assembly quality with frameshift errors

  question
  nf-core/viralrecon#528 · Filter by author YangJingqii opened on Oct 15, 2025