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QUANT: silent per-sample drop from order-dependent combine(by:) on groupKey

bugSomething isn't workingSomething isn't working

Status: Open.

#459 In nf-core/mhcquant;

· jonasscheid opened on Jun 3, 2026

v3.2.0: silent per-sample drop in QUANT subworkflow + OpenMS 3.5.0 FAIMS regression

bugSomething isn't workingSomething isn't working

Status: Open.

#458 In nf-core/mhcquant;

· alisa2alithea opened on Jun 1, 2026

timsTOF im2deep rescoring fails: tdf2mzml ion mobility (MS:1002814) not read by ms2rescore_rs

bugSomething isn't workingSomething isn't working

Status: Open.

#456 In nf-core/mhcquant;

· jonasscheid opened on May 22, 2026

UNTAR/UNZIP eval() version capture is broken — compressed .d input fails

bugSomething isn't workingSomething isn't working

Status: Open.

#452 In nf-core/mhcquant;

· jonasscheid opened on May 20, 2026

wiff format

questionFurther information is requestedFurther information is requested

Status: Open.

#423 In nf-core/mhcquant;

· wangjiawen2013 opened on Dec 15, 2025

result.pep.xml could not be found

questionFurther information is requestedFurther information is requested

Status: Open.

#422 In nf-core/mhcquant;

· EmaEtch opened on Dec 11, 2025

MS2Rescore config change to prevent crash on 16GB computer

questionFurther information is requestedFurther information is requested

Status: Open.

#421 In nf-core/mhcquant;

· rohitsuresh1407-cpu opened on Dec 1, 2025

DIA data and MHCII

questionFurther information is requestedFurther information is requested

Status: Open.

#420 In nf-core/mhcquant;

· wangjiawen2013 opened on Nov 21, 2025

How to speed up

questionFurther information is requestedFurther information is requested

Status: Open.

#418 In nf-core/mhcquant;

· wangjiawen2013 opened on Nov 20, 2025

Update docs with new subworkflows

Status: Open.

#398 In nf-core/mhcquant;

· jonasscheid opened on Sep 15, 2025

·  

3.3.0

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

enhancementNew feature or requestNew feature or request

Status: Open.

#377 In nf-core/mhcquant;

· jonasscheid opened on May 28, 2025

Port local OpenMS modules to nf-core modules

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#296 In nf-core/mhcquant;

· jonasscheid opened on Dec 21, 2023