Issues

• Request v2.3.1 patch release for Nextflow 25.04 compatibility

  nf-core/crisprseq#282 · Filter by author mulatta opened on Sep 21, 2026

• Add construct-aware paired-guide decoding to the screening workflow

  enhancement
  nf-core/crisprseq#278 · Filter by author Yifan1835 opened on Aug 3, 2026

• An error occurred when running the plotter.R script

  bug
  nf-core/crisprseq#275 · Filter by author sun-fei2026 opened on Jun 22, 2026
  1

• Lack of determinism in results across identical runs

  bug
  nf-core/crisprseq#269 · Filter by author alvaropvr opened on Feb 11, 2026
  4

• change in BAGEL2 fold-change calculation between crisprseq v2.3.0 and v2.4.0dev

  bug
  nf-core/crisprseq#265 · Filter by author metinyazar opened on Jan 28, 2026

• bowtie/align inconsistencies with latest NF version

  nf-core/crisprseq#264 · Filter by author mirpedrol opened on Nov 20, 2025

• Add details for samples sheet creation

  enhancement
  nf-core/crisprseq#250 · Filter by author tkolarik opened on Jun 18, 2025
  3

• More than one target per sample

  enhancementfeature-request
  nf-core/crisprseq#245 · Filter by author ashotmarg opened on May 5, 2025

• Add 2FAST2Q as an alternative to the MAGeCK count / Bowtie2 combo on the screening workflow

  enhancement
  nf-core/crisprseq#243 · Filter by author afombravo opened on Mar 31, 2025
  4

• JSON schema: Crisprseq

  documentation
  nf-core/crisprseq#242 · Filter by author jen-reeve opened on Mar 25, 2025

• fastq concatenation

  enhancement
  nf-core/crisprseq#241 · Filter by author matbonfanti opened on Mar 24, 2025

• add test for bowtie alignment

  enhancement
  nf-core/crisprseq#240 · Filter by author matbonfanti opened on Mar 24, 2025 · 3.0.0
  

• Allele frequencies for indels and edits

  enhancementfeature-request
  nf-core/crisprseq#217 · Filter by author dtatarak opened on Nov 15, 2024

• Pass DRUGZ in conda

  enhancement
  nf-core/crisprseq#189 · Filter by author LaurenceKuhl opened on Aug 1, 2024

• Sample not being detected as edited despite evidence of editing in the bam file

  bug
  nf-core/crisprseq#188 · Filter by author alan-tracey opened on Jul 25, 2024
  1

• MAGECK mle cnv correction doesn't work

  bug
  nf-core/crisprseq#179 · Filter by author LaurenceKuhl opened on Jul 22, 2024
  4

• Suggested addition: a PCA illustrating sample/condition/replicates

  enhancement
  nf-core/crisprseq#166 · Filter by author jeremymsimon opened on Jul 5, 2024

• ZeroDivisionError at alignment_summary.py stage due to low read number in input: mapped_reads_percentage = mapped_reads_count * 100 / total_reads_count

  bug
  nf-core/crisprseq#164 · Filter by author alan-tracey opened on Jul 4, 2024

• N characters introduced into *indels.csv

  bug
  nf-core/crisprseq#162 · Filter by author alan-tracey opened on Jul 4, 2024
  7

• Pass BAGEL2 in conda

  enhancement
  nf-core/crisprseq#155 · Filter by author LaurenceKuhl opened on Jun 14, 2024
  

• Add separate R scripts for local modules

  enhancement
  nf-core/crisprseq#154 · Filter by author LaurenceKuhl opened on Jun 14, 2024
  

• Integrate Chronos for screen data

  enhancement
  nf-core/crisprseq#112 · Filter by author j-andrews7 opened on Feb 2, 2024
  2

• Pass file to cutadapt

  enhancement
  nf-core/crisprseq#107 · Filter by author morriso1 opened on Jan 17, 2024
  2

• Update nf-core/modules/mageck/count

  enhancement
  nf-core/crisprseq#88 · Filter by author LaurenceKuhl opened on Nov 13, 2023

• UMI steps to subworkflows

  enhancementgood-first-issue
  nf-core/crisprseq#46 · Filter by author mirpedrol opened on Jun 27, 2023