Issues

• Pipeline fails with "Unknown process directive: echo" on Nextflow >= 26.05.0-edge

  nf-core/nanoseq#340 · Filter by author stefanoboriero opened on Sep 25, 2026

• curl not found when running with docker profile with jaffal fusion turn on

  bug
  nf-core/nanoseq#332 · Filter by author yinshiyi opened on Jan 27, 2026
  1

• DEEPVARIANT Model type for ONP data

  bug
  nf-core/nanoseq#331 · Filter by author full-metal-tech opened on Dec 17, 2025

• Minimap2 Option

  enhancement
  nf-core/nanoseq#328 · Filter by author cKeuters opened on Oct 6, 2025

• Can I use the pipeline on pacbio data?

  nf-core/nanoseq#325 · Filter by author sitems opened on Jun 18, 2025

• Error running nanoseq 3.1.0 with input_path to Nanopore fastq_pass directory

  bug
  nf-core/nanoseq#324 · Filter by author tamuanand opened on Jun 4, 2025
  2

• update nf-core modules already in pipeline

  enhancement
  nf-core/nanoseq#308 · Filter by author tzvi909 opened on Mar 24, 2025
  

• Liftover bedtools/gtf2bed from nf-core

  enhancement
  nf-core/nanoseq#307 · Filter by author tzvi909 opened on Mar 24, 2025

• Liftover to CuteSV nf-core module

  enhancement
  nf-core/nanoseq#306 · Filter by author mlgosh opened on Mar 24, 2025
  

• Liftover to Sniffles nf-core module

  enhancement
  nf-core/nanoseq#305 · Filter by author mlgosh opened on Mar 24, 2025

• Liftover to Medaka nf-core module

  enhancement
  nf-core/nanoseq#304 · Filter by author mlgosh opened on Mar 24, 2025
  

• Liftover to Deepvariant nf-core module

  enhancement
  nf-core/nanoseq#303 · Filter by author mlgosh opened on Mar 24, 2025

• Liftover to Graphmap2 nf-core module

  enhancement
  nf-core/nanoseq#302 · Filter by author mlgosh opened on Mar 24, 2025
  1

  

• liftover multiqc to nf-core module

  enhancement
  nf-core/nanoseq#301 · Filter by author slam2049 opened on Mar 24, 2025

• Liftover to MiniMap2 nf-core module

  enhancement
  nf-core/nanoseq#300 · Filter by author mlgosh opened on Mar 24, 2025
  

• Add uBAM alignment

  enhancement
  nf-core/nanoseq#298 · Filter by author cvriehl opened on Mar 24, 2025

• JSON schema: nanoseq

  nf-core/nanoseq#297 · Filter by author slam2049 opened on Mar 24, 2025

• Sniffles version creating malformed VCF files

  bug
  nf-core/nanoseq#294 · Filter by author callumjethomas opened on Mar 11, 2025
  1

• i have run the nanoseq pipeline and it is giving me this error, although i have run jaffal seperatly and it worked fine. i dont know why this issue occurrs while running the nanoseq pipeline.

  nf-core/nanoseq#293 · Filter by author usama-khan1998 opened on Jan 28, 2025

• fq.gz not staged correctly when skipping demultiplexing

  bug
  nf-core/nanoseq#291 · Filter by author CormacKinsella opened on Jan 22, 2025

• Add ToulligQC for raw read QC

  enhancement
  nf-core/nanoseq#285 · Filter by author Salome-Brunon opened on Nov 18, 2024

• java.lang.OutOfMemoryError: Java heap space with FastQC

  bug
  nf-core/nanoseq#283 · Filter by author jlandry69 opened on Oct 30, 2024
  1

• Nanoseq Pipeline Fails at Bambu Process with java.lang.Boolean Error

  nf-core/nanoseq#279 · Filter by author xeniaroda opened on Oct 7, 2024
  1

• Different Chromosome counts between samtools and bambu

  bug
  nf-core/nanoseq#278 · Filter by author fbndr98 opened on Oct 1, 2024

• FILTER 'STRANDBIAS' is not defined in the header

  bug
  nf-core/nanoseq#276 · Filter by author mazzalab opened on Sep 17, 2024