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Release 3.1.0 #401

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@jonasscheid jonasscheid commented Sep 17, 2025 •
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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
  • 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
MultiQC 1.28.0 1.31.0
Nf-core 3.2.1 3.4.1
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
@JuliaGraf
Add proteoform to pipeline output
6611217
@JuliaGraf
Update changelog
3cfc6f0
@JuliaGraf
Lint Changelog
f1a4385
@jonasscheid
Merge pull request #376 from JuliaGraf/proteoform
d332972
@nf-core-bot
Template update for nf-core/tools version 3.3.1
18a2222
@janaHoffmann1
initial commit
aae99a1
@jonasscheid
merge template
110bcef
@jonasscheid
add default snap
9c4bf03
@jonasscheid
fix ro-crate-metadata
ebfce73
@jonasscheid
fix maintainers
5dd26cf
@jonasscheid
fix some nf-core linting warnings and bump mqc version
7b9212c
@jonasscheid
fix default nf-test
c2447d4
@jonasscheid
fix trailing whitespace
2ce1816
@jonasscheid @maxulysse
nf-test.yml aktualisieren
e2702e7 
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
@jonasscheid
fix pyopenms version parsing, update snapshot
1f041cf
@jonasscheid
Merge branch 'template-merge-331' of https://github.com/jonasscheid/m…
2d657df 
…hcquant into template-merge-331
@jonasscheid
Put result file temporarily on ignore list due to float rounding inco…
6cceff2 
…nsistencies
@jonasscheid
Put result file temporarily on ignore list due to float rounding inco…
b05cd9f 
…nsistencies
@jonasscheid
add mqc_length_dist file to ignore list
cc7dcdf
@jonasscheid
update snapshot
1f5f47f
@JuliaGraf
Change lineplots to box plots
fc16d95
@JuliaGraf
Add peptide intensity box plots
21873d1
@JuliaGraf
Change to log2
abb9ae5
@jonasscheid
Update assets/multiqc_config.yml
c9478b5
@jonasscheid
Update CHANGELOG.md
adc185f
@jonasscheid
Merge pull request #382 from JuliaGraf/boxplots
b56ca9f 
Add box plots to the MulitQC report
@jonasscheid
Round all float values to 5 decimals to ensure stable checksums
a47b375
@jonasscheid
Merge branch 'dev' into template-merge-331
19f5607
@jonasscheid
Update base.config
61b50f5
@jonasscheid
Update CHANGELOG.md
7fd77ef
jonasscheid and others added 17 commits October 2, 2025 16:04
@jonasscheid
fix trailing whitespace
5ccdaef
@jonasscheid
add nf-core bot automations
772dea5
@jonasscheid
specify mhcquant as target repo
d38ea69
@jonasscheid
Update DOI to MHCquant2 publication
1d9eabe
@jonasscheid
add .vscode/settings.json to nf-core.yml to run nf-core pipelines lin…
46f7af4 
…t --fix rocrate_readme_sync without errors
@jonasscheid
update ro-create
b334333
@jonasscheid
Merge pull request #404 from nf-core/copilot/fix-20167b1f-b3d6-4467-b…
9cbef27 
…23b-a284a17c6709

Populate default values in nextflow_schema.json from nextflow.config params
Initial plan
c27bbb1
@jonasscheid
Change "false" to false in assets/multiqc_config.yml
27e3b78 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
@jonasscheid
Add changelog update script for CI integration
44dfa86 
This script updates the CHANGELOG.md based on PR title and number, ensuring entries are added correctly without duplication.
@jonasscheid
Merge pull request #407 from nf-core/copilot/fix-boolean-value-in-config
f3b745d
@jonasscheid
Implementation attempt to update-snapshots using nf-core bot
659eb7c
@jonasscheid
Delete .github/workflows/update-textual-snapshots.yml
813545e
@jonasscheid
Delete .github/workflows/changelog.yml
906babc
@jonasscheid
Merge pull request #406 from nf-core/update-doi
f553b79 
Update MHCquant2 publication DOI
@jonasscheid @mirpedrol
Update .github/workflows/update-snapshots.yml
22c6306 
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
@jonasscheid
Merge pull request #405 from nf-core/add-nfcore-bot
9e1e619 
Add nf-core bot to automate changelog, fix linting, update snapshots
@jonasscheid
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@nf-core-bot update snapshots

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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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@jonasscheid @nf-core-bot @JuliaGraf @janaHoffmann1 @steffenlem