feat: expose FDR conservative parameter by ypriverol · Pull Request #690 · bigbio/quantms

ypriverol · 2026-04-03T06:58:01Z

Summary

Add fdr_conservative parameter (default true) to control the FDR estimation formula in FalseDiscoveryRate
When true (default): uses (D+1)/T — conservative upper bound, backward compatible
When false: uses (D+1)/(T+D) — tighter estimate per Keich & Noble (2025, Nature Methods)

Motivation

In a benchmarking study comparing quantms against ProteomeDiscoverer on TMTpro 16-plex data, we traced a significant source of peptide loss to the conservative FDR formula. The (D+1)/T formula inflates q-values by ~20-40% compared to (D+1)/(T+D), which causes borderline peptides with good Percolator PEP scores (< 0.01) to be filtered out when the inflated q-value exceeds the PSM-level FDR cutoff.

Specifically, X PD-confirmed peptides had original Percolator PEP < 0.01 but were removed (we suspected) because the conservative FDR formula pushed their q-values above the 1% threshold.

The parameter was already available in the OpenMS FalseDiscoveryRate tool as -algorithm:conservative but was not exposed in the quantms workflow.

Changes

File	Change
`nextflow.config`	Added `fdr_conservative = true` default parameter
`modules/local/openms/false_discovery_rate/main.nf`	Pass `-algorithm:conservative ${params.fdr_conservative}`
`nextflow_schema.json`	Added schema entry with documentation

References

Keich U, Noble WS. On the use of entrapment to evaluate the false discovery rate in mass spectrometry-based proteomics. Nature Methods 22, 1454–1463 (2025)

Test plan

Default behavior (fdr_conservative=true) produces identical results to current version
Setting fdr_conservative=false reduces q-values and recovers additional peptides/proteins
FDR control remains valid with fdr_conservative=false (verify with entrapment or target-decoy analysis)

🤖 Generated with Claude Code

Add `fdr_conservative` parameter (default true for backward compatibility) that controls whether the FDR estimation uses the conservative formula (D+1)/T or the tighter (D+1)/(T+D). The conservative formula provides an upper bound on the true FDR but can be overly conservative, especially at low FDR thresholds. Keich & Noble (2025, Nature Methods) showed that (D+1)/T is useful for guaranteeing FDR control but inflates q-values by ~20-40% in the borderline range compared to (D+1)/(T+D). In benchmarking against ProteomeDiscoverer, we found that 429 PD-confirmed peptides with Percolator PEP < 0.01 were filtered out because the conservative FDR formula inflated their q-values above the 1% threshold. Setting fdr_conservative=false may recover a portion of these peptides while maintaining valid FDR control. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

coderabbitai · 2026-04-03T06:58:11Z

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 734a5aa8-8b4e-44eb-8e18-b157be5aa78c

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

Create PR with unit tests

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

qodo-code-review · 2026-04-03T06:58:14Z

Review Summary by Qodo

Expose FDR conservative parameter for flexible FDR estimation

✨ Enhancement

Walkthroughs

Description

• Expose fdr_conservative parameter to control FDR estimation formula
• Default true maintains backward compatibility with conservative (D+1)/T formula
• Setting false uses tighter (D+1)/(T+D) estimate per Keich & Noble (2025)
• Recovers peptides filtered by overly conservative q-value inflation

Diagram

flowchart LR
  A["fdr_conservative parameter"] -->|true| B["Conservative formula (D+1)/T"]
  A -->|false| C["Tighter formula (D+1)/(T+D)"]
  B --> D["Upper bound on FDR"]
  C --> E["Tighter q-value estimates"]
  D --> F["Backward compatible default"]
  E --> G["Recover borderline peptides"]

File Changes

1. modules/local/openms/false_discovery_rate/main.nf ✨ Enhancement +1/-0

Pass conservative parameter to FalseDiscoveryRate tool
• Added -algorithm:conservative ${params.fdr_conservative} flag to FalseDiscoveryRate command
• Passes the parameter value to OpenMS tool for FDR formula selection
modules/local/openms/false_discovery_rate/main.nf

2. nextflow.config ⚙️ Configuration changes +1/-0

Add fdr_conservative parameter with default value
• Added fdr_conservative = true parameter with default value
• Includes inline comment explaining the two FDR formula options
nextflow.config

3. nextflow_schema.json 📝 Documentation +7/-0

Document fdr_conservative parameter in schema

• Added schema entry for fdr_conservative boolean parameter
• Includes description, default value, icon, and detailed help text
• References Keich & Noble (2025) for FDR estimation methodology

nextflow_schema.json

qodo-code-review · 2026-04-03T06:58:15Z

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (2) 📎 Requirement gaps (0) 🎨 UX Issues (0)

1. Invalid schema JSON 🐞 Bug ≡ Correctness

Description

nextflow_schema.json is syntactically invalid because the newly added fdr_conservative property
block is not followed by a comma even though additional properties follow. Any consumer parsing the
schema will fail (e.g., nf-core launch / parameter schema validation tooling).

Code

nextflow_schema.json[R975-976]

+                },
                "protein_inference_debug": {

Evidence

In JSON, object properties must be comma-separated. Here, the fdr_conservative property closes and
the next property (protein_inference_debug) starts immediately on the next line with no comma,
making the file invalid JSON.

nextflow_schema.json[969-976]
nextflow_schema.json[976-980]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
`nextflow_schema.json` is invalid JSON because the `fdr_conservative` property definition is not followed by a comma, but another property (`protein_inference_debug`) follows immediately after.

## Issue Context
This breaks JSON parsing for any tooling that reads `nextflow_schema.json`.

## Fix
Add a trailing comma after the closing brace of the `fdr_conservative` property block.

## Fix Focus Areas
- nextflow_schema.json[969-976]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

2. fdr_conservative line too long 📘 Rule violation ⚙ Maintainability

Description

The new fdr_conservative parameter line is far over the ~120 character guideline, reducing
readability and violating the project’s Nextflow/Groovy style conventions. This can cause formatting
drift and makes reviews harder.

Code

nextflow.config[34]

+    fdr_conservative         = true   // Use (D+1)/T formula (true) or (D+1)/(T+D) (false) for FDR estimation

Evidence

PR Compliance ID 7 requires adhering to project code style conventions, including keeping lines
generally under ~120 characters. The newly added fdr_conservative line includes a long inline
comment that exceeds this guideline.

AGENTS.md
nextflow.config[34-34]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The `fdr_conservative` parameter line includes an inline comment that makes the line exceed the project’s preferred ~120 character limit.

## Issue Context
This is a style/readability requirement for Groovy/Nextflow code.

## Fix Focus Areas
- nextflow.config[34-34]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

3. fdr_conservative untested parameter 📘 Rule violation ☼ Reliability

Description

The PR changes module behavior by wiring params.fdr_conservative into the FalseDiscoveryRate
call, but no targeted test was added to exercise the new non-default behavior (false). This risks
regressions going undetected for the new feature.

Code

modules/local/openms/false_discovery_rate/main.nf[31]
+        -algorithm:conservative ${params.fdr_conservative} \\

Evidence

PR Compliance ID 8 requires workflow/module changes to be exercised by targeted tests and/or nf-test
cases. The diff adds a new runtime-affecting CLI flag controlled by params.fdr_conservative, but
the PR contains no corresponding test additions/updates to validate the new behavior.

AGENTS.md
modules/local/openms/false_discovery_rate/main.nf[31-31]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
The new `fdr_conservative` parameter path (`false`) is not covered by any targeted test changes in this PR.

## Issue Context
The module invocation now conditionally changes the FDR algorithm via `-algorithm:conservative ${params.fdr_conservative}`; the non-default behavior should be exercised in CI.

## Fix Focus Areas
- modules/local/openms/false_discovery_rate/main.nf[31-31]
- tests/default.nf.test[7-32]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

ⓘ The new review experience is currently in Beta. Learn more

codacy-production · 2026-04-03T06:59:07Z

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

View in Codacy

_{TIP This summary will be updated as you push new changes. Give us feedback}

qodo-code-review · 2026-04-03T07:01:55Z

nextflow_schema.json

+                },
                "protein_inference_debug": {


1. Invalid schema json 🐞 Bug ≡ Correctness

nextflow_schema.json is syntactically invalid because the newly added fdr_conservative property block is not followed by a comma even though additional properties follow. Any consumer parsing the schema will fail (e.g., nf-core launch / parameter schema validation tooling).

Agent Prompt

## Issue description `nextflow_schema.json` is invalid JSON because the `fdr_conservative` property definition is not followed by a comma, but another property (`protein_inference_debug`) follows immediately after. ## Issue Context This breaks JSON parsing for any tooling that reads `nextflow_schema.json`. ## Fix Add a trailing comma after the closing brace of the `fdr_conservative` property block. ## Fix Focus Areas - nextflow_schema.json[969-976]

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

Copilot

Pull request overview

Exposes an OpenMS FalseDiscoveryRate “conservative” toggle as a workflow parameter to control which FDR estimation formula is used, keeping the current behavior as the default.

Changes:

Add params.fdr_conservative (default true) to the pipeline configuration
Wire params.fdr_conservative into the OpenMS FalseDiscoveryRate invocation via -algorithm:conservative
Document the new parameter in nextflow_schema.json

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
nextflow_schema.json	Adds schema/documentation for the new `fdr_conservative` boolean parameter
nextflow.config	Introduces the default `fdr_conservative = true` pipeline parameter
modules/local/openms/false_discovery_rate/main.nf	Passes `params.fdr_conservative` through to OpenMS `FalseDiscoveryRate`

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ypriverol requested review from Copilot and jpfeuffer April 3, 2026 07:00

qodo-code-review bot reviewed Apr 3, 2026

View reviewed changes

Copilot AI reviewed Apr 3, 2026

View reviewed changes

Copilot started reviewing on behalf of ypriverol April 3, 2026 07:16 View session

ypriverol mentioned this pull request Apr 3, 2026

CI failure: OpenMS container cannot create config directory #691

Open

chore: update quantms-rescoring container to 0.0.16

48937af

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ypriverol merged commit 8427ac3 into bigbio:dev Apr 4, 2026
118 of 128 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

feat: expose FDR conservative parameter#690

feat: expose FDR conservative parameter#690
ypriverol merged 2 commits intobigbio:devfrom
ypriverol:feat/expose-fdr-conservative-param

ypriverol commented Apr 3, 2026 •

edited

Loading

Uh oh!

coderabbitai bot commented Apr 3, 2026 •

edited

Loading

Review skipped

Uh oh!

qodo-code-review bot commented Apr 3, 2026

Uh oh!

qodo-code-review bot commented Apr 3, 2026 •

edited

Loading

Uh oh!

codacy-production bot commented Apr 3, 2026 •

edited

Loading

Uh oh!

qodo-code-review bot Apr 3, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Milestone

Development

Uh oh!

2 participants

Conversation

ypriverol commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary

Motivation

Changes

References

Test plan

Uh oh!

coderabbitai bot commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Review skipped

Uh oh!

qodo-code-review bot commented Apr 3, 2026

Review Summary by Qodo

Walkthroughs

File Changes

Uh oh!

qodo-code-review bot commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Code Review by Qodo

Uh oh!

codacy-production bot commented Apr 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Up to standards ✅

Uh oh!

qodo-code-review bot Apr 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Milestone

Development

Uh oh!

2 participants

ypriverol commented Apr 3, 2026 •

edited

Loading

coderabbitai bot commented Apr 3, 2026 •

edited

Loading

qodo-code-review bot commented Apr 3, 2026 •

edited

Loading

codacy-production bot commented Apr 3, 2026 •

edited

Loading