Handling DIANN parameters to get extended parameters to modules validated by ypriverol · Pull Request #660 · bigbio/quantms

ypriverol · 2026-02-20T09:57:55Z

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coderabbitai · 2026-02-20T09:58:04Z

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Copilot

Pull request overview

This pull request enhances the DIA-NN workflow by adding support for custom command-line arguments via a new diann_extra_args parameter. The changes ensure that a single DIA-NN configuration file is shared across all DIA-NN processing steps, and introduce validation logic to prevent incompatible flags from being passed to specific DIA-NN steps.

Changes:

Added diann_extra_args parameter to allow users to pass custom DIA-NN arguments
Modified DIA workflow to convert the configuration channel to a value channel for reuse across multiple processes
Updated all DIA-NN modules (except INSILICO_LIBRARY_GENERATION) to receive and use the diann_config file for extracting modification flags
Implemented validation function to strip incompatible flags with warnings for each DIA-NN step

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
workflows/dia.nf	Converts diann_cfg to value channel and passes it to all DIA-NN modules that need it
modules/local/diann/preliminary_analysis/main.nf	Added diann_config input parameter and modification flag extraction logic
modules/local/diann/individual_analysis/main.nf	Added diann_config input parameter and modification flag extraction logic
modules/local/diann/final_quantification/main.nf	Added diann_config input parameter and modification flag extraction logic
modules/local/diann/assemble_empirical_library/main.nf	Added diann_config input parameter and modification flag extraction logic
conf/modules/modules.config	Added validateDiannExtraArgs function and updated ext.args for all DIA-NN steps to use it
nextflow.config	Added diann_extra_args parameter with default null value
nextflow_schema.json	Added schema definition for diann_extra_args parameter
ro-crate-metadata.json	Added clarification about supported SDRF file extensions (.sdrf, .tsv, .csv)
.gitignore	Added .claude/ directory to ignore list

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conf/modules/modules.config

modules/local/diann/preliminary_analysis/main.nf

modules/local/diann/individual_analysis/main.nf

modules/local/diann/final_quantification/main.nf

modules/local/diann/assemble_empirical_library/main.nf

modules/local/diann/preliminary_analysis/main.nf

modules/local/diann/individual_analysis/main.nf

modules/local/diann/assemble_empirical_library/main.nf

modules/local/diann/final_quantification/main.nf

jpfeuffer · 2026-02-20T10:29:19Z

In theory not bad. Did you ask at nf-core how other people solved that so far?
I think this approach will not work if people overwrite ext.args in their config, so the usefulness is limited to the diann_extra parameter.

ypriverol · 2026-02-20T10:30:58Z

In theory not bad. Did you ask at nf-core how other people solved that so far? I think this approach will not work if people overwrite ext.args in their config, so the usefulness is limited to the diann_extra parameter.

Im now in the nf-core channel discussing that.

Copilot

Pull request overview

Copilot reviewed 22 out of 23 changed files in this pull request and generated 15 comments.

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modules/local/diann/individual_analysis/main.nf

conf/modules/dia.config

ro-crate-metadata.json

CHANGELOG.md

README.md

modules/local/diann/preliminary_analysis/main.nf

modules/local/diann/assemble_empirical_library/main.nf

conf/modules/dia.config

modules/local/utils/msrescore_fine_tuning/main.nf

modules/local/utils/msrescore_features/main.nf

conf/modules/dia.config

jpfeuffer · 2026-02-21T15:39:52Z

modules/local/diann/insilico_library_generation/main.nf

+    blocked.sort { a -> -a.length() }.each { flag ->
+        def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
+        if (args =~ flagPattern) {
+            log.warn "DIA-NN: '${flag}' is managed by the pipeline for INSILICO_LIBRARY_GENERATION and will be stripped."


Maybe add some hint on where the actual parameters that manage that can be found.

I still think this should be addressed. "Managed by the pipeline" wont help users if they are trying to change a parameter and get that warning.

enryH · 2026-02-22T19:06:25Z

In theory not bad. Did you ask at nf-core how other people solved that so far? I think this approach will not work if people overwrite ext.args in their config, so the usefulness is limited to the diann_extra parameter.

Im now in the nf-core channel discussing that.

https://nfcore.slack.com/archives/CE6SDBX2A/p1771582947571129

enryH · 2026-02-22T19:08:50Z

Is DIANN updated?

ypriverol · 2026-02-24T12:22:23Z

This PR is related also with the new release of quantms refactoring going on: #663

Lukas-Neuhauser-HMS

Hi @ypriverol,

I went through the PR. It neatly serves our needs. I have no further comments.

Also, cool that you addressed that diann_normalize was not passed to DIANN before and that performance_mode does now not block ext.args of PRELIMINARY_ANALYSIS anymore.

Thank you!
Lukas

ypriverol · 2026-02-25T09:29:51Z

Thanks @Lukas-Neuhauser-HMS . Also for triggering more discussions in quantms #663 Please let us know if we have some more questions in those issues.

jpfeuffer

There is still an open comment about the relatively useless warnings.
And some concerning Github Copilot comments.

daichengxin · 2026-02-25T10:18:33Z

workflows/dia.nf

    // MODULE: INDIVIDUAL_ANALYSIS
    //
-    INDIVIDUAL_ANALYSIS(indiv_fin_analysis_in)
+    INDIVIDUAL_ANALYSIS(indiv_fin_analysis_in, ch_diann_cfg)


Do all DIA modules require the ch_diann_cfg parameter now, eg modifications?

Nice catch; let me double check this.

enryH · 2026-02-26T15:44:20Z

I was reading a bit on ext.args, and just want to add it as a reference here: https://nf-co.re/docs/contributing/components/ext_args

ypriverol added 3 commits February 20, 2026 08:15

changes in DIANN parameters

7967c82

Merge branch 'dev' of https://github.com/bigbio/quantms into dev

85ebfe9

Fix bug in DIANN

6a844fa

ypriverol requested review from Copilot and jpfeuffer February 20, 2026 09:58

ypriverol requested a review from daichengxin February 20, 2026 09:58

Copilot started reviewing on behalf of ypriverol February 20, 2026 09:59 View session

ypriverol linked an issue Feb 20, 2026 that may be closed by this pull request

Passing external arguments to DIA-NN workflow #640

Open

Copilot AI reviewed Feb 20, 2026

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ypriverol added 10 commits February 20, 2026 11:32

minor changes remove typing

dbcfa40

Minor changes inline parameters

a72b0ff

refactor modules config better for understanding

b153011

minor version error with conda

e681713

Template update for nf-core/tools version 3.5.2

1c2a413

Merge branch 'TEMPLATE' into dev

9222568

minor changes

73ae074

minorn change to fix rescoring issues

5f824fb

Fix the user issue in fine-tunning module

35ba535

better validation

0fbb097

ypriverol requested a review from Copilot February 20, 2026 19:07

Copilot started reviewing on behalf of ypriverol February 20, 2026 19:08 View session

Copilot AI reviewed Feb 20, 2026

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ypriverol mentioned this pull request Feb 20, 2026

Passing external arguments to DIA-NN workflow #640

Open

Minor changes to fix minor issues

80518d0

ypriverol changed the title ~~Changes in DIANN parameters~~ Handling DIANN parameters to get extended parameters to modules validated Feb 20, 2026

Fix but with normalization

95277e8

jpfeuffer reviewed Feb 21, 2026

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conf/modules/dia.config Show resolved Hide resolved

jpfeuffer reviewed Feb 21, 2026

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Lukas-Neuhauser-HMS approved these changes Feb 25, 2026

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ypriverol requested a review from jpfeuffer February 25, 2026 09:30

jpfeuffer requested changes Feb 25, 2026

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ypriverol mentioned this pull request Feb 25, 2026

Improve the documentation in for DIANN + quantms and modules parameters #673

Open

daichengxin reviewed Feb 25, 2026

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ypriverol added 2 commits February 25, 2026 20:23

Remove triqler and mzml stats

5658c73

Merge branch 'dev' of https://github.com/bigbio/quantms into dev

81f1ac1

ypriverol added 8 commits February 26, 2026 18:11

quantms-utils -> 0.0.25

724c084

updte hash for the container

f044477

minor issue of .d permissions

f0ae1ee

test from .d ready timsTOOF

34a5216

roolback change in msstats

392871c

Recover patch about permissions in ms2rescore

82c3947

minor changes in tests

151f9a9

skip msstats

80887cc

This was linked to issues Feb 28, 2026

TDF2MZML fails; running DIANN on .d files #672

Closed

Remove triqler from the outputs and the pipeline #674

Closed

mzTab for DIANN should be removed #675

Closed

ypriverol merged commit 9b4ea3a into bigbio:dev Mar 1, 2026
49 of 50 checks passed

This was referenced Mar 1, 2026

Remove triqler from the outputs and the pipeline #674

Closed

mzTab for DIANN should be removed #675

Closed

TDF2MZML fails; running DIANN on .d files #672

Closed

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ypriverol commented Feb 20, 2026

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