Issues

• Non-deterministic IDMerger input order (unsorted groupTuple)

  nf-core/mhcquant#489 · Filter by author jonasscheid opened on Oct 3, 2026

• wiff format

  question
  nf-core/mhcquant#423 · Filter by author wangjiawen2013 opened on Dec 15, 2025
  3

• result.pep.xml could not be found

  question
  nf-core/mhcquant#422 · Filter by author EmaEtch opened on Dec 11, 2025
  10

• MS2Rescore config change to prevent crash on 16GB computer

  question
  nf-core/mhcquant#421 · Filter by author rohitsuresh1407-cpu opened on Dec 1, 2025
  9

• DIA data and MHCII

  question
  nf-core/mhcquant#420 · Filter by author wangjiawen2013 opened on Nov 21, 2025
  1

• How to speed up

  question
  nf-core/mhcquant#418 · Filter by author wangjiawen2013 opened on Nov 20, 2025
  6

• Update docs with new subworkflows

  nf-core/mhcquant#398 · Filter by author jonasscheid opened on Sep 15, 2025 · 3.4.0
  

• Re-add optional vcf input for sample-specific database generation and search

  enhancement
  nf-core/mhcquant#377 · Filter by author jonasscheid opened on May 28, 2025
  

• Remove writing out all peaks when using Ion Annotator

  enhancement
  nf-core/mhcquant#286 · Filter by author jonasscheid opened on Oct 8, 2023 · 3.4.0