add IsobaricWorkflow to TMT workflow by MaLLLiYA · Pull Request #604 · bigbio/quantms

MaLLLiYA · 2025-10-30T10:40:04Z

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coderabbitai · 2025-10-30T10:40:14Z

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Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com>

jpfeuffer · 2025-10-31T07:53:38Z

This tool is not merged into dev yet.
I think you are building containers from dev only.

jpfeuffer · 2025-10-31T07:54:00Z

I merged it now. You still need new containers.

ypriverol · 2025-10-31T08:19:23Z

I need to build the container, give me the weekend.

Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com>

… into isobaric_workflow

qodo-code-review · 2026-04-03T10:14:07Z

Review Summary by Qodo

Integrate IsobaricWorkflow into TMT quantification pipeline

✨ Enhancement

Walkthroughs

Description

• Replace TMT workflow with IsobaricWorkflow module
• Simplify quantification pipeline by removing intermediate steps
• Add IsobaricWorkflow configuration parameters
• Update module configuration for result publishing

Diagram

flowchart LR
  ID["ID subworkflow"]
  ISO["ISOBARIC_WORKFLOW module"]
  CONV["MSSTATS_CONVERTER module"]
  MSSTATS["MSSTATS_TMT module"]
  
  ID -- "id_results" --> ISO
  ISO -- "consensusXML" --> CONV
  CONV -- "msstats output" --> MSSTATS

File Changes

1. conf/modules/modules.config ⚙️ Configuration changes +1/-1

Add IsobaricWorkflow to result publishing config
• Added ISOBARIC_WORKFLOW to the publishDir configuration for result tables
• Ensures isobaric workflow outputs are published to quant_tables directory
conf/modules/modules.config

2. modules/local/openms/isobaric_workflow/main.nf ✨ Enhancement +64/-0

Create IsobaricWorkflow process module

• New process module implementing OpenMS IsobaricWorkflow tool
• Handles isobaric labeling extraction and normalization from LC-MS/MS data
• Sorts input mzML and idXML files by base name for consistent processing
• Generates mzTab and consensusXML output files with version tracking

modules/local/openms/isobaric_workflow/main.nf

3. modules/local/openms/isobaric_workflow/meta.yml 📝 Documentation +42/-0

Add IsobaricWorkflow module metadata documentation

• New metadata file documenting IsobaricWorkflow module
• Defines inputs (mzML spectra, idXML identifications, experimental design)
• Specifies outputs (mzTab, consensusXML, log files, versions)
• References OpenMS documentation and tool homepage

modules/local/openms/isobaric_workflow/meta.yml

View more (2)

4. nextflow.config ⚙️ Configuration changes +3/-0

Add IsobaricWorkflow configuration parameters
• Added IsobaricWorkflow configuration section with type parameter
• Sets default isobaric labeling type to itraq4plex
nextflow.config

5. workflows/tmt.nf ✨ Enhancement +20/-25

Refactor TMT workflow to use IsobaricWorkflow

• Replaced multi-step workflow (FEATURE_MAPPER, FILE_MERGE, PROTEIN_INFERENCE, PROTEIN_QUANT) with
 single ISOBARIC_WORKFLOW module
• Added MSSTATS_CONVERTER module to convert consensusXML to msstats format
• Simplified channel operations by removing intermediate subworkflows
• Updated workflow outputs to use IsobaricWorkflow and MSSTATS_CONVERTER results

workflows/tmt.nf

qodo-code-review · 2026-04-03T10:14:08Z

Code Review by Qodo

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

1. Wrong label type source 🐞 Bug ≡ Correctness

Description

ISOBARIC_WORKFLOW passes the IsobaricWorkflow “-type” argument from params.type (default
itraq4plex), which is disconnected from the pipeline’s existing experiment label type
(meta.labelling_type / params.labelling_type), so TMT runs can be processed with the wrong plex
setting and yield incorrect quantification.

Code

modules/local/openms/isobaric_workflow/main.nf[R46-48]

+        -exp_design ${expdes} \\
+        -type ${params.type} \\
+        -inference_method ${params.protein_inference_method} \\

Evidence
The new IsobaricWorkflow wrapper uses params.type for the “-type” CLI argument, while the pipeline
already models the experiment’s labeling as labelling_type (stored in meta.labelling_type from SDRF
or params.labelling_type) and branches isobaric workflows based on that value. Existing isobaric
tooling (IsobaricAnalyzer) correctly uses meta.labelling_type for “-type”, demonstrating the
intended source of truth.
modules/local/openms/isobaric_workflow/main.nf[41-57]
nextflow.config[69-75]
nextflow.config[181-183]
subworkflows/local/create_input_channel/main.nf[102-114]
subworkflows/local/create_input_channel/main.nf[144-152]
workflows/quantms.nf[70-76]
modules/local/openms/isobaric_analyzer/main.nf[57-70]

Agent prompt

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

## Issue description
`ISOBARIC_WORKFLOW` passes `-type` from `params.type` (new, defaults to `itraq4plex`), but the pipeline already tracks the experiment label type as `labelling_type` (in `meta.labelling_type`, derived from SDRF or `params.labelling_type`). This can cause TMT experiments to run with the wrong `-type` value.

## Issue Context
- `meta.labelling_type` is the pipeline’s current source-of-truth for label type.
- `params.labelling_type` is already a top-level parameter.
- Introducing a separate `params.type` makes the behavior diverge from the rest of the pipeline.

## Fix Focus Areas
- modules/local/openms/isobaric_workflow/main.nf[41-57]
- workflows/tmt.nf[41-60]
- subworkflows/local/create_input_channel/main.nf[102-114]
- subworkflows/local/create_input_channel/main.nf[144-152]
- nextflow.config[69-75]
- nextflow.config[181-183]

## Suggested fix
1. Remove the new `params.type` (or at least stop using it).
2. Plumb the experiment’s labeling type into `ISOBARIC_WORKFLOW` and pass that to the tool:
  - Option A (preferred): add a `val labelling_type` input to the `ISOBARIC_WORKFLOW` process and compute it in `workflows/tmt.nf` from `ch_file_preparation_results` metadata (e.g., extract `it[0].labelling_type`, ensure it’s unique, then pass it).
  - Option B: use `params.labelling_type` if you also ensure it is populated for SDRF runs (currently SDRF sets `meta.labelling_type`, not necessarily `params.labelling_type`).
3. Update the IsobaricWorkflow invocation to `-type ${labelling_type}` (or `${meta.labelling_type}` if you decide to pass `meta`).

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

2. Broken module metadata layout 🐞 Bug ⚙ Maintainability

Description

modules/local/openms/isobaric_workflow/meta.yml lists inputs (mzmls/id_files/expdes) under the tools
section instead of a top-level input section, unlike other modules, so metadata consumers won’t
correctly identify the module’s inputs.

Code

modules/local/openms/isobaric_workflow/meta.yml[R6-23]

+tools:
+  - IsobaricWorkflow:
+      description: |
+        Extracts and normalizes isobaric labeling information from an LC-MS/MS experiment.
+      homepage: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+      documentation: https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_IsobaricWorkflow.html
+  - mzmls:
+      type: file
+      description: Input Spectra in mzML format
+      pattern: "*.mzML"
+  - id_files:
+      type: file
+      description: Identifications in idXML or mzIdentML format with posterior error probabilities as score type.
+      pattern: "*.idXML"
+  - expdes:
+      type: file
+      description: An experimental design file
+      pattern: "*.tsv"

Evidence
Existing module metadata in this repo declares inputs under a dedicated input: section, whereas
the new isobaric_workflow meta.yml places those entries under tools: and has no input: section
at all, making it inconsistent and likely to be misread by any tooling that expects the established
layout.
modules/local/openms/isobaric_workflow/meta.yml[6-24]
modules/local/openms/msstats_converter/meta.yml[6-22]
modules/local/openms/proteomicslfq/meta.yml[7-30]

Agent prompt

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

## Issue description
`modules/local/openms/isobaric_workflow/meta.yml` declares `mzmls`, `id_files`, and `expdes` under `tools:` instead of under a top-level `input:` section. This diverges from other module meta.yml files in the repository and prevents consistent discovery of module inputs.

## Issue Context
Compare with `modules/local/openms/msstats_converter/meta.yml` and `modules/local/openms/proteomicslfq/meta.yml`, which both use `tools:` only for the actual tool and use a separate `input:` section for input files.

## Fix Focus Areas
- modules/local/openms/isobaric_workflow/meta.yml[1-41]
- modules/local/openms/msstats_converter/meta.yml[1-35]
- modules/local/openms/proteomicslfq/meta.yml[1-56]

## Suggested fix
- Keep only `IsobaricWorkflow` under `tools:`.
- Add a top-level `input:` section and move the `mzmls`, `id_files`, and `expdes` entries there (mirroring the layout used by other OpenMS modules in this repo).

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

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qodo-code-review · 2026-04-03T10:21:00Z

+        -exp_design ${expdes} \\
+        -type ${params.type} \\
+        -inference_method ${params.protein_inference_method} \\


1. Wrong label type source 🐞 Bug ≡ Correctness

ISOBARIC_WORKFLOW passes the IsobaricWorkflow “-type” argument from params.type (default itraq4plex), which is disconnected from the pipeline’s existing experiment label type (meta.labelling_type / params.labelling_type), so TMT runs can be processed with the wrong plex setting and yield incorrect quantification.

Agent Prompt

## Issue description `ISOBARIC_WORKFLOW` passes `-type` from `params.type` (new, defaults to `itraq4plex`), but the pipeline already tracks the experiment label type as `labelling_type` (in `meta.labelling_type`, derived from SDRF or `params.labelling_type`). This can cause TMT experiments to run with the wrong `-type` value. ## Issue Context - `meta.labelling_type` is the pipeline’s current source-of-truth for label type. - `params.labelling_type` is already a top-level parameter. - Introducing a separate `params.type` makes the behavior diverge from the rest of the pipeline. ## Fix Focus Areas - modules/local/openms/isobaric_workflow/main.nf[41-57] - workflows/tmt.nf[41-60] - subworkflows/local/create_input_channel/main.nf[102-114] - subworkflows/local/create_input_channel/main.nf[144-152] - nextflow.config[69-75] - nextflow.config[181-183] ## Suggested fix 1. Remove the new `params.type` (or at least stop using it). 2. Plumb the experiment’s labeling type into `ISOBARIC_WORKFLOW` and pass that to the tool: - Option A (preferred): add a `val labelling_type` input to the `ISOBARIC_WORKFLOW` process and compute it in `workflows/tmt.nf` from `ch_file_preparation_results` metadata (e.g., extract `it[0].labelling_type`, ensure it’s unique, then pass it). - Option B: use `params.labelling_type` if you also ensure it is populated for SDRF runs (currently SDRF sets `meta.labelling_type`, not necessarily `params.labelling_type`). 3. Update the IsobaricWorkflow invocation to `-type ${labelling_type}` (or `${meta.labelling_type}` if you decide to pass `meta`).

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

add IsobaricWorkflow to TMT workflow

66080bb

Merge branch 'dev' into isobaric_workflow

3765937

jpfeuffer requested changes Oct 30, 2025

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Comment thread workflows/tmt.nf Outdated

ypriverol and others added 2 commits October 30, 2025 21:43

Update workflows/tmt.nf

3ec6c72

Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Merge branch 'dev' into isobaric_workflow

70c60e4

ypriverol and others added 4 commits November 4, 2025 07:26

Update workflows/tmt.nf

f369833

Co-authored-by: Julianus Pfeuffer <8102638+jpfeuffer@users.noreply.github.com>

pre-commit

2a33101

Improvement of IsobaricWorkflow

d560a37

Merge branch 'dev' into isobaric_workflow

e6c1c41

MaLLLiYA changed the base branch from dev to dev_IsobaricWorkflow December 18, 2025 01:53

MaLLLiYA added 2 commits December 18, 2025 10:20

pre-commit

881a69a

Merge branch 'isobaric_workflow' of https://github.com/MaLLLiYA/quantms…

e7d22b1

… into isobaric_workflow

ypriverol marked this pull request as ready for review April 3, 2026 10:13

ypriverol merged commit fc363bb into bigbio:dev_IsobaricWorkflow Apr 3, 2026
16 of 26 checks passed

ypriverol mentioned this pull request Apr 3, 2026

fix: IsobaricWorkflow - auto-detect labelling type, pass isotope correction and extraction params #693

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add IsobaricWorkflow to TMT workflow#604

add IsobaricWorkflow to TMT workflow#604
ypriverol merged 10 commits intobigbio:dev_IsobaricWorkflowfrom
MaLLLiYA:isobaric_workflow

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MaLLLiYA commented Oct 30, 2025

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