Issues

• config file error?

  bug
  nf-core/cutandrun#318 · Filter by author gaodifan opened on Sep 15, 2026

• prepare_genome fails if the gtf annotation contains large chromosome

  bug
  nf-core/cutandrun#314 · Filter by author JKing2000 opened on Jul 23, 2026

• spikein_bowtie2 parameter incorrectly assigned to iGenomes Bowtie index when using local spikein_fasta

  bug
  nf-core/cutandrun#313 · Filter by author tylerstahl opened on Jun 3, 2026

• Resource allocations for several tools are excessive

  bug
  nf-core/cutandrun#310 · Filter by author spvensko opened on Apr 15, 2026

• Nextflow 25.10.4 fails with Cannot invoke method optional() on null object in TRIMGALORE module (nf-core/cutandrun v3.2.2)

  bug
  nf-core/cutandrun#309 · Filter by author susannbruche opened on Mar 18, 2026
  1

• deeptools PCA not transposed

  nf-core/cutandrun#308 · Filter by author laurie-tonon opened on Mar 3, 2026

• matplotlib temp file

  bug
  nf-core/cutandrun#305 · Filter by author sunta3iouxos opened on Dec 4, 2025

• duplicates are always removed

  bug
  nf-core/cutandrun#304 · Filter by author sunta3iouxos opened on Nov 27, 2025

• Pipeline failure if a sample has zero alignments

  bugpipeline_error
  nf-core/cutandrun#303 · Filter by author HDash opened on Nov 25, 2025

• test run TRIMGALORE error

  bug
  nf-core/cutandrun#301 · Filter by author JakobHofvander opened on Oct 23, 2025
  6

• TODO list for 3.3.0 release

  enhancement
  nf-core/cutandrun#300 · Filter by author maxulysse opened on Oct 21, 2025 · 3.3.0
  1

• Consesus peaks

  enhancement
  nf-core/cutandrun#298 · Filter by author sunta3iouxos opened on Oct 10, 2025
  2

• cutandrun pipeline reflects density across individual reads rather than read pairs (?)

  bug
  nf-core/cutandrun#297 · Filter by author fansalon opened on Oct 1, 2025

• NFCORE_CUTANDRUN:CUTANDRUN:FILTER_READS:SAMTOOLS_VIEW

  bug
  nf-core/cutandrun#295 · Filter by author kartikeyasingh1 opened on Aug 28, 2025

• find_unique_reads.py keeps lower-scoring duplicates instead of highest MAPQ

  bug
  nf-core/cutandrun#293 · Filter by author HDash opened on Aug 22, 2025
  

• Discrepancy between MACS2 and SEACR-called peaks

  bug
  nf-core/cutandrun#292 · Filter by author mdozmorov opened on Aug 12, 2025
  2

• Why is there no FRiP score section in my MultiQC report?

  bug
  nf-core/cutandrun#291 · Filter by author RnapolyMerase1212 opened on Aug 10, 2025
  1

• Accept gzipped custom genomes via --gtf and --fasta

  enhancement
  nf-core/cutandrun#286 · Filter by author smoe opened on May 19, 2025
  1

• Saved input bams for MACS2?

  nf-core/cutandrun#285 · Filter by author bhanco opened on May 6, 2025
  1

• Unexpected Inclusion of Bisulfite_Genome/ Files in Bowtie2 Alignment Step

  bug
  nf-core/cutandrun#282 · Filter by author edogiuili opened on Apr 1, 2025

• JSON schema: Cutandrun

  documentation
  nf-core/cutandrun#280 · Filter by author jen-reeve opened on Mar 25, 2025
  

• Could you please share the SVG file of the worflow subway diagram?

  nf-core/cutandrun#278 · Filter by author yinshiyi opened on Mar 13, 2025

• implementation of fastp and implementation of extra trim arguments

  enhancement
  nf-core/cutandrun#277 · Filter by author sunta3iouxos opened on Mar 11, 2025

• Strange error

  enhancement
  nf-core/cutandrun#275 · Filter by author stela2502 opened on Feb 26, 2025

• Understanding Spike-In Alignment Decisions

  nf-core/cutandrun#274 · Filter by author NikoBlank opened on Feb 10, 2025
  3