Add per-sample search parameter support via samplesheet by jonasscheid · Pull Request #439 · nf-core/mhcquant

jonasscheid · 2026-02-06T14:06:30Z

Summary

This PR adds support for per-sample search parameters in the samplesheet, enabling users to combine samples with different MHC classes, instruments, or search strategies in a single pipeline run. Crucial step towards SDRF-Support #277.

Key Features

SearchPreset column: Choose from predefined presets (lumos/qe/timstof/astral/xl × class1/class2)
TSV-based preset definitions: Presets defined in assets/search_presets.tsv with JSON schema validation
Full parameter priority chain: CLI params > preset > nextflow.config defaults
Preset-aware global FDR: Groups by search preset for proper FDR control
Search params propagated end-to-end: From samplesheet through CometAdapter, MS2Rescore, Percolator, IDFilter

Parameter Priority

Search parameters are resolved with the following priority (highest to lowest):

CLI parameters (--fragment_mass_tolerance 0.05) — override everything
Search preset (SearchPreset column → assets/search_presets.tsv) — predefined parameter sets
Config defaults (nextflow.config) — global fallback

CLI override detection uses workflow.commandLine regex matching to determine if a parameter was explicitly set.

Search Preset Parameters

Each preset defines the following parameters:

Parameter	Description	Example
`PeptideMinLength` / `PeptideMaxLength`	Peptide length filters	8 / 14
`PrecursorMassRange`	Digest mass range	800:2500
`PrecursorCharge`	Precursor charge states	2:3
`PrecursorMassTolerance`	Precursor mass tolerance	5
`PrecursorErrorUnit`	Tolerance unit (ppm/Da)	ppm
`FragmentMassTolerance`	Fragment mass tolerance	0.01
`FragmentBinOffset`	Fragment binning offset	0.0
`MS2PIPModel`	MS2Rescore model	Immuno-HCD
`ActivationMethod`	Fragmentation method	HCD
`Instrument`	Instrument resolution	high_res
`NumberMods`	Max variable modifications	3
`FixedMods` / `VariableMods`	Modification lists	Oxidation (M)

Available Presets

Preset	Instrument	Class	Key Settings
`lumos_class1` / `qe_class1` / `astral_class1`	Orbitrap	I	8-14 AA, HCD, high_res
`lumos_class2` / `qe_class2` / `astral_class2`	Orbitrap	II	8-30 AA, HCD, high_res
`timstof_class1`	timsTOF	I	8-14 AA, CID, 20 ppm
`timstof_class2`	timsTOF	II	8-30 AA, CID, 20 ppm
`xl_class1` / `xl_class2`	LTQ/XL	I/II	CID, low_res, 0.5 Da frag

Users can also provide a custom presets TSV via --search_presets.

Implementation Details

assets/search_presets.tsv — TSV file with 10 predefined presets
assets/schema_search_presets.json — JSON schema for preset validation (with meta key mappings)
resolveSearchParams() in utils_nfcore_mhcquant_pipeline/main.nf — priority resolution: CLI > preset > default
conf/modules.config — CometAdapter/MS2Rescore/IDFilter use meta.X for search params
mhcquant.nf — passes full search meta into RESCORE via dynamic key subtraction
rescore/main.nf — strips search params on emit to maintain downstream join compatibility

Testing

✅ Default test profile passes
✅ Search presets test (test_search_presets) — stable with full peptidoform snapshot
✅ Per-sample parameters correctly applied through CometAdapter, MS2Rescore, IDFilter
✅ Global FDR preset grouping verified

Use Case Example

ID  Sample  Condition  ReplicateFileName    SearchPreset
1   HepG2   ClassI     sample1.mzML         qe_class1
2   HepG2   ClassI     sample2.mzML         qe_class1
3   HepG2   ClassII    sample3.mzML         qe_class2
4   Jurkat  ClassI     sample4.mzML         timstof_class1

This allows combining Class I and Class II samples, or different instruments, in a single run with appropriate parameters for each. A CLI override like --fragment_mass_tolerance 0.05 would override all presets globally.

Checklist

This PR is against the dev branch
Pipeline tests pass
Schema validation passes
Code follows nf-core best practices
Nextflow strict syntax compliant

…plesheet # Conflicts: # modules.json # modules/local/easypqp/convert/main.nf # modules/local/easypqp/library/main.nf # modules/local/epicore/main.nf # modules/local/ms2rescore/main.nf # modules/local/openms/featurefinderidentification/main.nf # modules/local/openms/idconflictresolver/main.nf # modules/local/openms/idmassaccuracy/main.nf # modules/local/openms/mapaligneridentification/main.nf # modules/local/openms/maprttransformer/main.nf # modules/local/openms/mztabexporter/main.nf # modules/local/openms/psmfeatureextractor/main.nf # modules/local/openms/textexporter/main.nf # modules/local/openmsthirdparty/featurelinkerunlabeledkd/main.nf # modules/local/openmsthirdparty/percolatoradapter/main.nf # modules/local/pyopenms/chromatogramextractor/main.nf # modules/local/pyopenms/ionannotator/main.nf # modules/local/tdf2mzml/main.nf # modules/local/untar/main.nf # modules/local/unzip/main.nf # modules/nf-core/openms/idmassaccuracy/tests/main.nf.test # subworkflows/local/map_alignment/main.nf # subworkflows/local/prepare_spectra/main.nf # subworkflows/local/process_feature/main.nf # subworkflows/local/rescore/main.nf # subworkflows/local/speclib/main.nf

- Add 12 optional search parameter columns to schema_input.json (SearchPreset, PeptideMinLength, PeptideMaxLength, PrecursorMassRange, PrecursorCharge, etc.) - Add resolveSearchParams() with priority: individual column > preset > global params - Add search_presets.config with 8 presets (lumos/qe/timstof/xl x class1/class2) - Convert Sample/Condition integers to strings during samplesheet parsing - Add test_search_params profile to nextflow.config

- Apply meta.X ?: params.X pattern for per-sample parameter override in CometAdapter, IDFilter, MS2Rescore, IDMassAccuracy, and IonAnnotator - Add -weights flag to PERCOLATORADAPTER_GLOBAL to avoid filename collisions

- Carry search_preset through ch_rescore_in in mhcquant.nf - Group by preset in RESCORE for IDMERGER_GLOBAL and backfilter via combine(by:0) - Fix EASYPQP_LIBRARY multi-include syntax in speclib subworkflow

- Change Channel.empty() to channel.empty() (lowercase) - Replace implicit 'it' with explicit closure parameter in EPICORE call

nf-core-bot · 2026-02-06T14:07:04Z

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.

- Update test_search_params.config to use nf-core/test-datasets samplesheet - Add tests/search_params.nf.test with snapshot - Remove local samplesheets folder (now using test-datasets)

…ile directive - Rename config, test file, and profile from search_params to search_presets - Add profile directive to nf-test file matching other test patterns - Use test-datasets samplesheet URL, remove local samplesheet - Use string concatenation for fasta path matching test.config pattern

…sheet

…commented lines - Restore nf-core modules to match upstream/dev - Remove emit declarations from version topic outputs in local modules - Remove version emit metadata from local module meta.yml files - Add peptidoform content check to search_presets nf-test

…napshot - Format schema_input.json with prettier - Add search_presets to schema_params lint ignore (nested config map) - Update ionannotator snapshot for topic channel version deduplication

…ence

…set > default priority

jonasscheid · 2026-02-09T09:16:43Z

@nf-core-bot fix linting

…p pipeline_if_empty_null

…search params

…ded defaults

…resets

conf/modules.config

nextflow.config

subworkflows/local/rescore/main.nf

…clarify FDR comment

…ation on NF 25.04

…ce type, update snapshots

…put schema

…1, make test robust

nextflow.config

.nf-core.yml

docs/usage.md

… docs, update fragment tolerance

axelwalter

I like the new simplification by removing the custom parameters from the sample sheet and just keeping the preset column and optional override with CLI params. This approach is straight forward and removes confusion on which settings apply and also de-clutters the sample sheets significantly.

jonasscheid and others added 11 commits January 23, 2026 20:43

Update openms and openmsthirdparty nf-core modules

6f93d36

Update local modules to use topic channels for versions

8f939b7

Remove redundant version parsing and channel creation from subworkflows

d0b1b82

Merge branch 'nf-core:dev' into dev

49c0b78

Merge branch 'dev' of https://github.com/jonasscheid/mhcquant into dev

c6c4269

Use meta-based search parameters in module configs

100aa29

- Apply meta.X ?: params.X pattern for per-sample parameter override in CometAdapter, IDFilter, MS2Rescore, IDMassAccuracy, and IonAnnotator - Add -weights flag to PERCOLATORADAPTER_GLOBAL to avoid filename collisions

Group global FDR by search preset instead of merging all samples

c823c07

- Carry search_preset through ch_rescore_in in mhcquant.nf - Group by preset in RESCORE for IDMERGER_GLOBAL and backfilter via combine(by:0) - Fix EASYPQP_LIBRARY multi-include syntax in speclib subworkflow

Add test profile and samplesheet for search params feature

146f77b

Fix deprecated Nextflow syntax for strict mode compliance

15fb6ac

- Change Channel.empty() to channel.empty() (lowercase) - Replace implicit 'it' with explicit closure parameter in EPICORE call

jonasscheid added 10 commits February 6, 2026 14:21

Update CHANGELOG for per-sample search parameters feature

22e930d

Add nf-test for search params and use test-datasets samplesheet

2efdd68

- Update test_search_params.config to use nf-core/test-datasets samplesheet - Add tests/search_params.nf.test with snapshot - Remove local samplesheets folder (now using test-datasets)

Merge remote-tracking branch 'upstream/dev' into search-params-sample…

570bc7f

…sheet

Fix CI failures: prettier formatting, lint ignore, and ionannotator s…

52b1591

…napshot - Format schema_input.json with prettier - Add search_presets to schema_params lint ignore (nested config map) - Update ionannotator snapshot for topic channel version deduplication

Add search_presets as hidden param in nextflow_schema.json to fix lint

d6ad64e

Document per-sample search parameters and fix stale ch_versions refer…

06184be

…ence

Align search preset fragment_mass_tolerance with recommended settings

11c1926

Remove duplicate comment in mhcquant workflow

7985ec6

jonasscheid marked this pull request as ready for review February 9, 2026 07:50

jonasscheid requested a review from marissaDubbelaar as a code owner February 9, 2026 07:50

jonasscheid added 2 commits February 9, 2026 08:54

Propagate search params through pipeline with CLI > samplesheet > pre…

103bcf5

…set > default priority

Update docs/usage.md with CLI > samplesheet > preset > default priority

87179c8

jonasscheid added 3 commits February 9, 2026 10:16

Fix lint: move search_param_defaults into resolveSearchParams and ski…

bbf7eb1

…p pipeline_if_empty_null

Fix CLI override detection and add fixed/variable mods as per-sample …

7a174c4

…search params

Use workflow.commandLine for CLI override detection instead of hardco…

793e24e

…ded defaults

jonasscheid added 2 commits February 10, 2026 20:58

Update snapshots and fix invalid input parameter warning for search_p…

9f8ac95

…resets

Fix ion annotator join key mismatch and rename XL preset comment

b8a882b

axelwalter reviewed Feb 11, 2026

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jonasscheid added 7 commits February 12, 2026 11:49

Address PR review: fix mods tokenization, revert fixed_mods default, …

83a1fd5

…clarify FDR comment

Add search_presets back to defaultIgnoreParams to fix nf-schema valid…

3217313

…ation on NF 25.04

Add TSV validation to search_presets schema, fix PrecursorMassToleran…

01c2f5a

…ce type, update snapshots

Add search_presets.tsv, remove old search_presets.config, simplify in…

92f3f4b

…put schema

Update search_presets test for qe/lumos groups with stable snapshot

2ae3aa6

Add PrecursorErrorUnit to presets, fix fragment_mass_tolerance to 0.0…

8669e50

…1, make test robust

Capture full peptidoform content in search_presets snapshot

b813fc4

jonasscheid commented Feb 13, 2026

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jonasscheid commented Feb 13, 2026

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jonasscheid commented Feb 13, 2026

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jonasscheid commented Feb 13, 2026

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jonasscheid and others added 2 commits February 13, 2026 16:27

Address PR review comments: remove defaultIgnoreParams hack, simplify…

5d5a595

… docs, update fragment tolerance

Merge branch 'dev' into search-params-samplesheet

337b1da

axelwalter approved these changes Feb 27, 2026

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jonasscheid merged commit 951739d into nf-core:dev Feb 27, 2026
30 of 33 checks passed

jonasscheid deleted the search-params-samplesheet branch February 27, 2026 10:29

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Add per-sample search parameter support via samplesheet#439

Add per-sample search parameter support via samplesheet#439
jonasscheid merged 37 commits intonf-core:devfrom
jonasscheid:search-params-samplesheet

jonasscheid commented Feb 6, 2026 •

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jonasscheid commented Feb 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Summary

Key Features

Parameter Priority

Search Preset Parameters

Available Presets

Implementation Details

Testing

Use Case Example

Checklist

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jonasscheid commented Feb 9, 2026

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jonasscheid commented Feb 6, 2026 •

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