Release 3.1.0

[jonasscheid]

3.1.0 - BlüBa - 07/01/26

Added

• Added a peptidoform column to the pipeline output #376
• Added Boxplot of intensity distributions to the MulitQC report #382
• Added a config option to hide outliers in box plots, add plot descriptions #387
• Added a Fasta column to the input samplesheet to enable sample-specific FASTA files #391
• Added a column for unique accessions to the pipeline output #403

Fixed

• Fixed an issue with not providing the full process name in conf/base.config #384
• Template update 3.1.1, migrate to nf-test #379
• Fixed the binning of the TICs histogram and move the general stats table to the top of the report #388
• Write out FDR-filtered peptide list in global FDR-mode, instead of 100% FDR list #394
• Update labels for global FDR process configurations #397
• Remove special character '#' from the header of OpenMS TextExporter output #403
• Fixed an issue in the summary process that led the pipeline crash if deeplc was not specified #411

Dependencies

Dependency	Old version	New version
EasyPQP	0.1.51	0.1.53
Epicore		0.1.6
MultiQC	1.28.0	1.31.0
Nf-core	3.2.1	3.4.1
OpenMS	3.4.0	3.4.1

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[Aratz]

Nice work!

I left a few comments but I think for this release the most important ones are to fix the citations.

The other comments concern mostly tests and readability, and could also be addressed in a later release, I leave it up to you how you want to keep track of and address them :)

[rolivella]

@jonasscheid very good job! Just only a few concerns and comments. :)