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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

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

Dependencies

Dependency Old version New version
MultiQC 1.28.0 1.30.0
Nf-core 3.2.1 3.3.2
EasyPQP 0.1.51 0.1.53

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).

JuliaGraf and others added 30 commits May 26, 2025 16:36
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
Add box plots to the MulitQC report
JuliaGraf and others added 25 commits September 23, 2025 15:28
Add unique_accessions column and remove special character '#' from the OpenMS TextExporter output
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
…23b-a284a17c6709

Populate default values in nextflow_schema.json from nextflow.config params
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
This script updates the CHANGELOG.md based on PR title and number, ensuring entries are added correctly without duplication.
Update MHCquant2 publication DOI
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
Add nf-core bot to automate changelog, fix linting, update snapshots
@jonasscheid
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@nf-core-bot update snapshots

jonasscheid and others added 3 commits October 17, 2025 11:38
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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6 participants