Issues

• Add 5-bases Illumina kit support

  enhancement
  nf-core/methylseq#619 · Filter by author Mathias-Boulanger opened on Jul 24, 2026

• Adopt combined-index Bismark alignment modes / rethink the --multicore default (Bismark 3.1.0)

  enhancement
  nf-core/methylseq#615 · Filter by author FelixKrueger opened on Jul 15, 2026
  3

• Calling variants with rastair in the TAPS branch

  enhancement
  nf-core/methylseq#611 · Filter by author davidmasp opened on Jul 11, 2026
  3

  

• bwameth symlink bug

  bug
  Bug

  nf-core/methylseq#608 · Filter by author AlexUOM opened on May 6, 2026
  6

• --igenomes_base could not validate file format

  bug
  nf-core/methylseq#605 · Filter by author Blondeau-Bidet opened on Apr 21, 2026

• Add sample methylation summary for the Methyldackel workflow

  enhancement
  nf-core/methylseq#601 · Filter by author luigilamparelli opened on Mar 23, 2026

• speed issues

  nf-core/methylseq#600 · Filter by author chuddy-ibk opened on Mar 20, 2026

• Bismark alignment failure (0% mapping) caused by Bowtie2 2.5.5 regression with EM-seq paired-end parameters

  bug
  nf-core/methylseq#599 · Filter by author milcs40 opened on Mar 16, 2026

• bwa-mem aligner not using GPU

  enhancement
  nf-core/methylseq#597 · Filter by author ruochiz opened on Mar 3, 2026

• PICARD_COLLECTHSMETRICS process is skipped due to empty input channel

  bug
  nf-core/methylseq#596 · Filter by author bounlu opened on Feb 26, 2026

• Option --unmapped does not run Bismark with --unmapped argument

  bug
  nf-core/methylseq#595 · Filter by author thomasbleazard opened on Jan 20, 2026

• Resume function is re-doing alignments instead of resuming at methylation calls

  nf-core/methylseq#594 · Filter by author kingakotulska opened on Jan 19, 2026
  2

• Inconsistent explanations about "--zymo" in methylseq v4.2.0 documentation

  bug
  nf-core/methylseq#591 · Filter by author Winbuntu opened on Dec 18, 2025
  1

• Workflow exits after TrimGalore with “successful” status but no alignments produced

  bug
  nf-core/methylseq#589 · Filter by author sansense opened on Dec 9, 2025
  9

• conflicting advice in usage document

  bug
  nf-core/methylseq#588 · Filter by author sansense opened on Dec 9, 2025
  1

• [bug] - samplesheet schema for genome field too strict

  nf-core/methylseq#587 · Filter by author feiloo opened on Dec 9, 2025

• Support multiple bed files for targeted sequencing analysis

  enhancement
  nf-core/methylseq#573 · Filter by author bounlu opened on Oct 27, 2025

• Running in -stub mode fails for BISMARK_SUMMARY

  bug
  nf-core/methylseq#527 · Filter by author bounlu opened on May 9, 2025
  1

• Bismark soft clip --local_alignment True keeps L,value,value

  bug
  nf-core/methylseq#472 · Filter by author garefalaki opened on Nov 27, 2024
  1

• Add minimap2 as aligner option for Bismark

  enhancement
  nf-core/methylseq#455 · Filter by author FelixKrueger opened on Nov 12, 2024

• Specify additional "genomes" of spike-in controls for downstream calculation of bisulfite conversion efficiency

  enhancement
  nf-core/methylseq#394 · Filter by author pdemko opened on Apr 1, 2024
  7

  

• Support for NuGEN Ovation RRBS

  stale
  nf-core/methylseq#376 · Filter by author jma1991 opened on Jan 19, 2024
  2

• Add rastair

  enhancement
  nf-core/methylseq#374 · Filter by author bounlu opened on Jan 16, 2024
  1

  

• Mapping samples to multiple reference fasta

  dsl2enhancement
  nf-core/methylseq#181 · Filter by author rbpisupati opened on Nov 30, 2020
  15

• Complexity curve

  questionstale
  nf-core/methylseq#96 · Filter by author bazyliszek opened on May 21, 2019
  5