Issues

• Blacklist filtering improvement

  enhancement
  nf-core/atacseq#465 · Filter by author jpintar opened on Sep 30, 2026

• Unspecified Behavior for Mixed single-end and paired-end samples in one samplesheet

  bug
  nf-core/atacseq#464 · Filter by author NicoDeVeaux opened on Sep 30, 2026
  1

• MutliQC pinned in two places, with different versions.

  bug
  nf-core/atacseq#463 · Filter by author NicoDeVeaux opened on Sep 28, 2026

• Add nf-test coverage for --shift_reads and make conf/modules.config changes trigger CI tests

  enhancement
  nf-core/atacseq#462 · Filter by author fbnrst opened on Sep 25, 2026

• Fragment length filtering not applied when shifting merged_replicate BAMs (--shift_reads)

  bug
  nf-core/atacseq#460 · Filter by author fbnrst opened on Sep 25, 2026

• FRiP score overcounts reads that overlap more than one peak (intersectBed -c summed)

  bug
  nf-core/atacseq#458 · Filter by author fbnrst opened on Sep 25, 2026

• Optional UMI-aware preprocessing for UMI-ATAC-seq (--with_umi)

  enhancement
  nf-core/atacseq#456 · Filter by author ftabaro opened on Sep 11, 2026
  1

• Update nf-core modules to latest, and fix subsequent breaking subworkflow input signatures

  nf-core/atacseq#447 · Filter by author NicoDeVeaux opened on Jun 23, 2026

• The Usage section said use tab-delimited file but the samplesheet is actually comma-delimited

  bug
  nf-core/atacseq#444 · Filter by author endeneon opened on May 31, 2026

• Error running with "Error nextflow.config:298:14: Unexpected input"

  bug
  nf-core/atacseq#442 · Filter by author cyz0315 opened on May 19, 2026
  3

• BWA_MEM silently receives 0 tasks when BWA index is built from FASTA (no pre-built index provided)

  bug
  nf-core/atacseq#438 · Filter by author JoseEspinosa opened on Mar 25, 2026

• Docker: deprecate docker.userEmulation and use docker.runOptions; mitigates Trim Galore pipe freeze

  bug
  nf-core/atacseq#435 · Filter by author yxkwgp opened on Feb 27, 2026

• Generate complete snapshots for all tests

  enhancement
  nf-core/atacseq#427 · Filter by author JoseEspinosa opened on Oct 24, 2025
  

• limiting to NFR in the dev version

  nf-core/atacseq#424 · Filter by author BingbingYuan opened on Jul 29, 2025

• Error executing process

  bug
  nf-core/atacseq#421 · Filter by author arugula2388 opened on May 21, 2025

• several peaks correspond to the same gene

  nf-core/atacseq#418 · Filter by author BOBOL513 opened on Apr 7, 2025

• JSON schema: Atacseq

  nf-core/atacseq#416 · Filter by author kshirlekar opened on Mar 24, 2025
  

• Picard modules fail when all memory used

  bug
  nf-core/atacseq#415 · Filter by author JoseEspinosa opened on Mar 13, 2025 · 2.2

• CSI Implementation for Larger Genomes

  enhancement
  nf-core/atacseq#414 · Filter by author emilytrybulec opened on Mar 6, 2025 · 2.2
  1

• Number of cores calculation for Trimgalore

  wontfix
  nf-core/atacseq#413 · Filter by author PramodRaoB opened on Feb 25, 2025
  1

• ataqv

  question
  nf-core/atacseq#411 · Filter by author arugula2388 opened on Feb 10, 2025
  2

• Merged Replicates-Feature counts does not use the merged bams

  bug
  nf-core/atacseq#410 · Filter by author SuhasSrinivasan opened on Feb 1, 2025

• Support for Read Lengths Not in {50, 100, 150, 200}

  enhancement
  nf-core/atacseq#408 · Filter by author MikeKazz opened on Jan 24, 2025

• FastQC uses only 10 cores in a 32 core server

  enhancement
  nf-core/atacseq#404 · Filter by author SuhasSrinivasan opened on Jan 15, 2025
  2

• Please change default MACS2 peak calling to narrow peak

  enhancement
  nf-core/atacseq#403 · Filter by author SuhasSrinivasan opened on Jan 12, 2025
  2