Release 3.2.0

[jonasscheid]

3.2.0 - Solitude - 20/05/26

Added

• Added support for single run quantification #438
• Added per-sample search parameter support via samplesheet with SearchPreset column #439
• Added PRIDE ID and SDRF sheet support #445
• Added ion mobility export and MultiQC distribution plot for timsTOF data #441

Fixed

• Fixed crashes in FeatureLinkerUnlabeledKD and PYOPENMS_IONANNOTATOR for samples with zero peptides past FDR; empty samples now emit an empty TSV #451
• Fixed OPENMS_FILECONVERTER version eval emitting a \x01 control character into the MultiQC versions YAML due to an unescaped sed backreference #451
• Fixed nf-test CI failures caused by Docker layer extraction running out of disk space when pulling ms2rescore and OpenMS 3.5.0 containers; added jlumbroso/free-disk-space cleanup step and bumped the RunsOn disk to volume=40gb #451
• Fixed EPICORE running only once instead of per sample when --fasta is used, by broadcasting ch_fasta to EPICORE via .first() #446
• Fixed SUMMARIZE_RESULTS crash with --quantify caused by OpenMS 3.5.0 TextExporter phantom column bug (OpenMS/OpenMS#9120) #444
• Fixed an issue where stripping the sequence in SUMMARIZE_RESULTS did not work for complex modifications #436
• Fixed tdf2mzml container entrypoint issue by pinning to 0.5_noentry and invoking the CLI explicitly #447
• Fixed OPENMS_FILECONVERTER version extraction emitting a SOH byte due to a single-backslash sed backreference #447
• Fixed OPENMS_IDMASSACCURACY process argument to use meta.precursor_error_units so per-sample preset overrides apply #447

Changed

• Migrate to topic channels #431
• Bumped openms/fileconverter, openms/featurefinderidentification and openms/idconflictresolver local modules to OpenMS 3.5.0 #447
• Rewrote openms/idmassaccuracy meta.yml to reflect the actual process I/O #447
• Tightened preset normalization so empty/whitespace FixedMods and VariableMods cells are treated as empty (preserves the existing -fixed_modifications CLI call) #447
• Migrated conf/test_single_quant.config from deprecated max_cpus/max_memory/max_time to process.resourceLimits #447
• Replaced local openms/textexporter module with the nf-core/modules equivalent; preserved the _exported output suffix via ext.prefix to keep SUMMARIZE_RESULTS input/output filenames distinct #447
• Replaced local openms/fileconverter module with the nf-core/modules equivalent; updated PROCESS_FEATURE to consume the renamed converted output channel #449
• Replaced local pridepy/fetch_sdrf module with the nf-core/modules pridepy/fetchsdrf equivalent (now meta-aware); bumped local pridepy/download_file to pridepy 0.0.15 to match #449
• Sealed search-preset values: when a samplesheet row sets SearchPreset, preset values are no longer overridable via --<param>, -params-file, or -c for that row; rows without a preset resolve from params as before. Removed the fragile workflow.commandLine regex from resolveSearchParams (renamed to resolvePresetParams). Documented the new precedence in docs/usage.md. #449

Dependencies

Dependency	Old version	New version
easypqp	0.1.53	0.1.57
MultiQC	1.31.0	1.33.0
Nf-core	3.4.1	3.5.1
openms	3.4.1	3.5.0
tdf2mzml	0.3.0	0.5.0

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).

[jonasscheid]

@pinin4fjords Could we go in with the release now? The two failing tests are CI artifacts which randomly occur sometimes. I'm retriggering, but not sure how long it takes until gh is happy

[jonasscheid]

Thanks!!

[jonasscheid]

@nickp60

Without having tried the pipeline, the changes look good to me! Do you think the warning "Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred" is causing the directory deletion issue that's failing the singularity tests?

I think this is just a warning of apptainer accepting the legacy singularity env variable. Afaik ships with nf-core template..

Are there any remaining blocking requests from your side?

[nickp60]

@nickp60

Without having tried the pipeline, the changes look good to me! Do you think the warning "Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred" is causing the directory deletion issue that's failing the singularity tests?

I think this is just a warning of apptainer accepting the legacy singularity env variable. Afaik ships with nf-core template..

Are there any remaining blocking requests from your side?

no nothing on my end!

[jonasscheid]

Great! Could you hit the approve button then? ;)