Release 3.2.0 prep: PR #447 review fixes + textexporter migration

[jonasscheid]

Description

Release 3.2.0 preparation. Implements review feedback from PR #447 and migrates the local openms/textexporter module to its nf-core/modules equivalent.

Fixed (from PR #447 review)

• HIGH: OPENMS_FILECONVERTER version extraction emitted a SOH byte because the sed backref used \1 (single backslash) in Groovy — switched to \\1, matching every other OpenMS module.
• HIGH: OPENMS_IDMASSACCURACY meta.yml was a copy-paste of openms_idfilter — rewritten to reflect the actual (meta, mzmls, idxmls) → frag_err + optional prec_err signature.
• MED: OPENMS_IDMASSACCURACY config read params.precursor_error_units — changed to meta.precursor_error_units so per-sample preset overrides apply.
• LOW: Tab indent in modules/local/openms/idmassaccuracy/main.nf normalized to spaces.

Changed

• Bumped openms/fileconverter, openms/featurefinderidentification, openms/idconflictresolver local modules from OpenMS 3.4.1 → 3.5.0 (container openms:3.5.0--h78fb946_0). idmassaccuracy stays on 3.4.1 — IDMassAccuracy.cpp was removed in OpenMS 3.5.0.
• Migrated openms/textexporter from local → nf-core/modules. The nf-core module drops the _exported suffix from the output filename, which collided with the SUMMARIZE_RESULTS input. Injected ext.prefix = { \"\${meta.id}_exported\" } in conf/modules.config to preserve the distinct-filename invariant.
• Tightened preset normalization at utils_nfcore_mhcquant_pipeline/main.nf:135. nf-schema parses empty TSV cells as ArrayList [] (not null), so ?.trim() threw Unknown method invocation 'trim' on ArrayList type. Replaced with a type-safe check. Also emptied literal single-space FixedMods cells in assets/search_presets.tsv.
• The reviewer-suggested "mirror -fixed_modifications after -variable_modifications" change was flagged as cosmetic but actually changes the CometAdapter CLI: passing -fixed_modifications \ (empty value) vs omitting the flag produces different Comet search results (confirmed via search_presets.nf.test — peptidoforms shifted). Reverted, keeping the pre-release CLI behavior.
• tests/sdrf.nf.test → added tag \"test_sdrf\" for shard targeting.
• tests/test_single_quant.nf.test → renamed tag single_replicate → test_single_quant to match profile-name convention.
• conf/test_single_quant.config → migrated deprecated max_cpus/max_memory/max_time to process.resourceLimits.
• Removed unused validateInputSamplesheet function from utils_nfcore_mhcquant_pipeline/main.nf (confirmed no callers).
• Version bumped 3.2.0dev → 3.2.0 (via nf-core pipelines bump-version). Snapshot v3.2.0dev strings updated across all 7 tests/*.nf.test.snap files.

Dependencies

Dependency	Old	New
openms (three local modules)	3.4.1	3.5.0

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint). — 480 passed / 64 warnings (pre-existing subworkflow meta.yml missing) / 0 failures.
• Ensure the test suite passes. All 7 nf-tests ran green pre-textexporter-migration (default, mokapot, ionannotator, speclib, test_single_quant, sdrf, search_presets). default.nf.test re-run post-migration also passed (351s). Remaining tests skipped per user request.
• CHANGELOG.md is updated.
• Usage Documentation in docs/usage.md is updated. — No user-facing changes.
• Output Documentation in docs/output.md is updated. — No user-facing changes.
• README.md is updated. — No new tools/authors.

Follow-up notes

• Release name placeholder [release name] still in CHANGELOG.md:6 — needs filling before tag.
• openms/psmfeatureextractor can't be migrated to nf-core/modules without pipeline rework (local takes a second feature_file input and awks out an -extra flag; upstream takes idxml only).
• openms/idmassaccuracy has no viable upstream migration (deprecated in OpenMS 3.5.0+).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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.

[jonasscheid]

@pinin4fjords Ok for you if we proceed with 3.2.0 release and the 3.3.0 release includes the remaining openms tools ported to nf-core? I see even more value in porting the easypqp tools then

[pinin4fjords]

I really don't think you should be actively adding to local modules except for highly pipeline-specific stuff. As I mentioned on the release review I wasn't going to push you to migrate existing locals right now, but the four new ones from #447 are different:

• openms/fileconverter - the upstream slot exists right next to the other openms wrappers
• pridepy/download_file
• pridepy/fetch_sdrf
• sdrf_pipelines/parse_sdrf

What's the major blocker for those going in nf-core/modules first?

I do also worry that you've left the CLI override handling in resolveSearchParams untouched, I don't think it'll work well for the reasons in the differentialabundance PR I linked, and I don't want us setting precedent with things that people more knowledgable than myself have said are a really bad plan!

[jonasscheid]

I do also worry that you've left the CLI override handling in resolveSearchParams untouched, I don't think it'll work well for the reasons in the differentialabundance PR I linked, and I don't want us setting precedent with things that people more knowledgable than myself have said are a really bad plan!

I forgot to address this one, sorry about that

What's the major blocker for those going in nf-core/modules first?

The openms fileconverter is a simple addition that I can do. I did not add the pridepy and sdrf_pipelines tool yet to nf-core, since they are in an earlier development phase and subject to more fundamental changes. Pridepy did change the command namings and depricated some quite fast (https://github.com/PRIDE-Archive/pridepy#cli-command-overview) and therefore I thought that we will first test it for some time locally and see if the packages mature well, before we create more overhead with updating and depricating nf-core modules