Issues

• Start the pipeline after barcode tagging

  enhancement
  Enhancement

  nf-core/scnanoseq#113 · Filter by author wufishy opened on Sep 7, 2026
  3

• Fix error when running stub

  enhancement
  nf-core/scnanoseq#108 · Filter by author atrull314 opened on Jun 26, 2026

• Re-configure the modules.config

  enhancement
  nf-core/scnanoseq#107 · Filter by author atrull314 opened on Jun 26, 2026

• Automated conda test generates files that don't appear locally

  bug
  nf-core/scnanoseq#106 · Filter by author atrull314 opened on Jun 26, 2026

• Investigate default warning when running nf-test for conda

  bug
  nf-core/scnanoseq#105 · Filter by author atrull314 opened on Jun 26, 2026
  1

• Replace modules with nf-core versions

  enhancement
  nf-core/scnanoseq#104 · Filter by author atrull314 opened on Jun 11, 2026

• Convert specific local modules to nf-core/modules

  enhancement
  nf-core/scnanoseq#102 · Filter by author lianov opened on May 29, 2026

• Evaluate toulligqc for subsample data

  bug
  nf-core/scnanoseq#99 · Filter by author atrull314 opened on May 5, 2026

• Evaluate GPU integration where possible

  enhancement
  nf-core/scnanoseq#92 · Filter by author lianov opened on Mar 11, 2026
  1

  

• Pipe line fails at dedupe step possibly due to contigs with no read maps.

  bug
  nf-core/scnanoseq#89 · Filter by author wufishy opened on Jan 12, 2026
  6

• TAG_BARCODES produces empty tagged.bam on PacBio long-read data, causing BAMTOOLS_SPLIT to fail

  question
  nf-core/scnanoseq#88 · Filter by author camip2001-coder opened on Dec 22, 2025
  1

• The job always hangs at one particular step in the Slurm system.

  bug
  nf-core/scnanoseq#82 · Filter by author xyz202310 opened on Sep 24, 2025
  10

• Evaluate BLAZE's barcode correction

  enhancement
  nf-core/scnanoseq#75 · Filter by author lianov opened on Jul 21, 2025

• Number of final mapped reads and soft-clipping

  bug
  nf-core/scnanoseq#72 · Filter by author lauratwomey opened on Jun 20, 2025
  2

• Optimize GROUP_TRANSCRIPTS process

  enhancement
  nf-core/scnanoseq#71 · Filter by author atrull314 opened on Jun 17, 2025

• Exposing parameters to control barcode and UMI length for datasets generated with technologies other than 10X Genomics

  enhancement
  nf-core/scnanoseq#66 · Filter by author wendelljpereira opened on May 14, 2025
  3