nf-core/mhcquant

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Identify and quantify MHC eluted peptides from mass spectrometry raw data

Stars: 51
Forks: 35
Open beginner issues: 0
Indexed issues: 13
Avg merge: 1d 10h
Merged PRs (30d): 7

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

Open All

13 open issues indexed

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

bug

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/mhcquant#459 · Opened Jun 3, 2026
v3.2.0: silent per-sample drop in QUANT subworkflow + OpenMS 3.5.0 FAIMS regression Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/mhcquant#458 · 4 comments · 1 reaction · Opened Jun 1, 2026
timsTOF im2deep rescoring fails: tdf2mzml ion mobility (MS:1002814) not read by ms2rescore_rs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/mhcquant#456 · 1 comment · Opened May 22, 2026
UNTAR/UNZIP eval() version capture is broken — compressed .d input fails Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/mhcquant#452 · 1 comment · Opened May 20, 2026
wiff format Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/mhcquant#423 · 3 comments · Opened Dec 15, 2025
result.pep.xml could not be found Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/mhcquant#422 · 9 comments · Opened Dec 11, 2025
MS2Rescore config change to prevent crash on 16GB computer Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/mhcquant#421 · 9 comments · Opened Dec 1, 2025
DIA data and MHCII Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/mhcquant#420 · 1 comment · Opened Nov 21, 2025
How to speed up Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/mhcquant#418 · 6 comments · Opened Nov 20, 2025
Update docs with new subworkflows Open

nf-core/mhcquant#398 · 1 assignee · Opened Sep 15, 2025
Re-add optional vcf input for sample-specific database generation and search Open

enhancement

nf-core/mhcquant#377 · 1 assignee · Opened May 28, 2025
Port local OpenMS modules to nf-core modules Open

enhancement help wanted

nf-core/mhcquant#296 · 1 assignee · Opened Dec 21, 2023
Remove writing out all peaks when using Ion Annotator Open

enhancement

nf-core/mhcquant#286 · 1 assignee · Opened Oct 8, 2023

nf-core/mhcquant

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