Issues

• MACS3 is reporting that 100 paired reads are needed, even when single end data is used as input

  bug
  nf-core/chipseq#524 · Filter by author MingL196 opened on Jul 9, 2026
  2

• Change simple fasq_align_{aligner} subworkflows to fastq_align_dna

  nf-core/chipseq#511 · Filter by author Kevin-Brockers opened on Apr 30, 2026 · 2.3

• Switch local/module GTF2BED to nf-core/module BEDOPS_GTF2BED

  enhancement
  nf-core/chipseq#494 · Filter by author Kevin-Brockers opened on Mar 20, 2026 · 2.3

• Clarify genome size error and update usage documentation

  bug
  nf-core/chipseq#478 · Filter by author adthrasher opened on Nov 4, 2025 · 2.2-bug-fixes

• Port bedtools_genomecov from local to nf-core module

  enhancementimprove-behaviour
  Task

  nf-core/chipseq#469 · Filter by author FloWuenne opened on Jun 24, 2025 · 2.3

• Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun)

  enhancement
  nf-core/chipseq#463 · Filter by author wanisajad opened on May 16, 2025 · 2.3

• JSON schema: Chipseq

  docs
  nf-core/chipseq#458 · Filter by author jen-reeve opened on Mar 25, 2025 · 2.3
  

• Enable the use of CSI bam index

  enhancement
  nf-core/chipseq#454 · Filter by author JoseEspinosa opened on Mar 12, 2025 · 2.3
  2

• Output .bed file not found in the MACS2 folder

  enhancement
  nf-core/chipseq#448 · Filter by author GopishankarThirumoorthy opened on Feb 3, 2025 · 2.3
  1

• Adjust x-axis to start at 1 for custom phantompeakqualtools NSC plot

  enhancement
  nf-core/chipseq#441 · Filter by author pontushojer opened on Dec 17, 2024 · 2.3

• Get rid of checksamplesheet.py and switch to nf-schema

  enhancement
  nf-core/chipseq#403 · Filter by author JoseEspinosa opened on Jul 19, 2024 · 2.3

• Add --only_step options

  enhancement
  nf-core/chipseq#337 · Filter by author IStevant opened on Mar 8, 2023 · 2.3

• Spike ins normalization

  enhancement
  nf-core/chipseq#321 · Filter by author EmanuelSoda opened on Oct 28, 2022 · 2.3
  13

• Find test dataset where PRESEQ doesn't fail

  enhancement
  nf-core/chipseq#276 · Filter by author drpatelh opened on May 9, 2022 · 2.3
  2

  

• Output bigwigs with macs2 p-value signal for every base-pair

  enhancementfeature-request
  nf-core/chipseq#251 · Filter by author Al-Murphy opened on Feb 3, 2022 · 2.3
  4

• Merged biological replicates

  enhancement
  nf-core/chipseq#213 · Filter by author ryanmboileau opened on May 3, 2021 · 2.3

• Add IDR analysis

  enhancementfeature-request
  nf-core/chipseq#87 · Filter by author drpatelh opened on May 30, 2019 · 2.3
  5