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

[ypriverol]

Summary

Fixes several issues in the IsobaricWorkflow integration (PR #604) to make it ready for merge:

• Auto-detect labelling type from SDRF instead of hardcoded params.type='itraq4plex'. The labelling_type is extracted from the meta channel (already parsed from SDRF), matching how IsobaricAnalyzer works.
• Pass isotope correction matrix when params.isotope_correction is enabled, using the same correction matrix parsing logic as IsobaricAnalyzer
• Pass extraction parameters (min_precursor_purity, precursor_isotope_deviation, min_reporter_intensity) that were missing from the IsobaricWorkflow invocation
• Remove unused type parameter from nextflow.config (no longer needed since type is auto-detected)

Changes

File	Change
modules/local/openms/isobaric_workflow/main.nf	Add labelling_type input, isotope correction matrix handling, extraction params
workflows/tmt.nf	Extract labelling_type from meta channel and pass to IsobaricWorkflow
nextflow.config	Remove hardcoded type = 'itraq4plex'

Test plan

• Run with TMT16plex dataset — verify labelling_type is correctly auto-detected
• Run with isotope_correction enabled — verify correction matrix is passed
• Run with iTRAQ4plex dataset — verify 4-plex correction matrix format works

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[qodo-code-review]

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Review Summary by Qodo

Auto-detect IsobaricWorkflow labelling type and pass correction parameters

🐞 Bug fix ✨ Enhancement

Walkthroughs

Description

• Auto-detect labelling type from SDRF metadata instead of hardcoded parameter
• Pass isotope correction matrix when enabled, matching IsobaricAnalyzer behavior
• Add missing extraction parameters to IsobaricWorkflow invocation
• Remove unused hardcoded type parameter from configuration

Diagram

flowchart LR
  SDRF["SDRF metadata"]
  META["Meta channel<br/>labelling_type"]
  TMT["TMT workflow"]
  ISO["IsobaricWorkflow<br/>process"]
  PARAMS["Extraction &<br/>correction params"]
  
  SDRF -- "auto-detected" --> META
  META -- "extracted" --> TMT
  TMT -- "labelling_type" --> ISO
  PARAMS -- "passed" --> ISO

Loading

File Changes

1. modules/local/openms/isobaric_workflow/main.nf ✨ Enhancement +24/-1

Add dynamic labelling type and correction parameters

• Add labelling_type as input parameter to process
• Implement isotope correction matrix parsing and formatting based on labelling type
• Replace hardcoded params.type with dynamic labelling_type input
• Add missing extraction parameters: min_precursor_purity, precursor_isotope_deviation,
 min_reporter_intensity

modules/local/openms/isobaric_workflow/main.nf

---

2. workflows/tmt.nf ✨ Enhancement +5/-2

Extract and pass labelling type to workflow

• Extract labelling_type from meta channel in multiMap operation
• Pass extracted labelling_type as first argument to ISOBARIC_WORKFLOW process
• Use .first() to get single labelling type value from channel

workflows/tmt.nf

---

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

Remove unused hardcoded type parameter

• Remove hardcoded type = 'itraq4plex' parameter from IsobaricWorkflow configuration section

nextflow.config

---

[qodo-code-review]

Code Review by Qodo

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

1. Isotope correction silently skipped 🐞 Bug ≡ Correctness

Description

In ISOBARIC_WORKFLOW, enabling params.isotope_correction without setting
params.plex_corr_matrix_file results in no isotope-correction flags being passed to
IsobaricWorkflow, producing uncorrected reporter quantification without any error. This differs from
ISOBARIC_ANALYZER, which hard-fails when the matrix path is missing, making the workflow behavior
inconsistent and error-prone.

Code

modules/local/openms/isobaric_workflow/main.nf[R42-58]

+    // Build isotope correction matrix argument if enabled
+    def isotope_correction = ""
+    if (params.isotope_correction && params.plex_corr_matrix_file != null) {
+        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
+            .findAll { !it.startsWith('#') && it.trim() }
+            .drop(1)
+            .collect { line ->
+                def values = line.split('/')
+                if (labelling_type == 'tmt18plex' || labelling_type == 'tmt16plex') {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}/${values[5]}/${values[6]}/${values[7]}/${values[8]}\""
+                } else {
+                    return "\"${values[1]}/${values[2]}/${values[3]}/${values[4]}\""
+                }
+            }
+        def correction_matrix = matrix_lines.join(" ")
+        isotope_correction = "-quantification:isotope_correction true -${labelling_type}:correction_matrix ${correction_matrix}"
+    }

Evidence

ISOBARIC_WORKFLOW only constructs the isotope correction CLI flags when both
params.isotope_correction and params.plex_corr_matrix_file are set; otherwise it leaves the
interpolated ${isotope_correction} empty, so the tool runs without correction even though the user
enabled it. ISOBARIC_ANALYZER explicitly errors if isotope_correction is enabled but
plex_corr_matrix_file is null, demonstrating the intended contract and highlighting the
inconsistency.

modules/local/openms/isobaric_workflow/main.nf[42-58]
modules/local/openms/isobaric_workflow/main.nf[60-80]
modules/local/openms/isobaric_analyzer/main.nf[28-35]
nextflow_schema.json[776-785]

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` silently omits isotope-correction flags when `params.isotope_correction` is true but `params.plex_corr_matrix_file` is null. This produces incorrect (uncorrected) quantification without failing.

### Issue Context
`ISOBARIC_ANALYZER` already enforces the expected contract by erroring when `isotope_correction` is enabled but the matrix file is missing. `ISOBARIC_WORKFLOW` should match that behavior.

### Fix Focus Areas
- modules/local/openms/isobaric_workflow/main.nf[42-58]
- modules/local/openms/isobaric_workflow/main.nf[60-79]
- modules/local/openms/isobaric_analyzer/main.nf[28-35]

### Suggested fix
- If `params.isotope_correction` is true and `params.plex_corr_matrix_file` is null/empty, `error("plex_corr_matrix_file is required when isotope_correction is enabled")`.
- Optionally mirror `ISOBARIC_ANALYZER` and always pass `-quantification:isotope_correction true/false` explicitly for clarity/consistency.

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

---

2. Missing matrix path validation 🐞 Bug ☼ Reliability

Description

ISOBARIC_WORKFLOW reads the correction matrix using new
File(params.plex_corr_matrix_file).readLines() without checking existence or producing a friendly
error, so a wrong path fails as an unhandled FileNotFoundException during task script construction.
This reduces reliability and debuggability compared to explicit pipeline validation used elsewhere.

Code

modules/local/openms/isobaric_workflow/main.nf[R44-46]

+    if (params.isotope_correction && params.plex_corr_matrix_file != null) {
+        def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
+            .findAll { !it.startsWith('#') && it.trim() }

Evidence

The module directly reads the matrix path via java.io.File without a guard; if the path is
incorrect, Groovy will throw at readLines() (often surfacing as a stack trace rather than a clear
Nextflow error). In contrast, other inputs in the pipeline are explicitly checked for existence with
a clear message before continuing.

modules/local/openms/isobaric_workflow/main.nf[44-46]
subworkflows/local/create_input_channel/main.nf[97-100]

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` reads `params.plex_corr_matrix_file` with `new File(...).readLines()` without validating that the file exists. Misconfiguration yields a cryptic runtime exception.

### Issue Context
The pipeline already performs explicit existence checks for other user-provided file paths.

### Fix Focus Areas
- modules/local/openms/isobaric_workflow/main.nf[44-46]
- subworkflows/local/create_input_channel/main.nf[97-100]

### Suggested fix
- Before `readLines()`, validate that `params.plex_corr_matrix_file` points to an existing file and fail with `error("...")` including the bad path.
- (Optional) also validate basic format (e.g., ensure after filtering+drop(1) the matrix has at least one line) to avoid IndexOutOfBounds errors later.

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

---

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[qodo-code-review]

1. Isotope correction silently skipped 🐞 Bug ≡ Correctness

In ISOBARIC_WORKFLOW, enabling params.isotope_correction without setting
params.plex_corr_matrix_file results in no isotope-correction flags being passed to
IsobaricWorkflow, producing uncorrected reporter quantification without any error. This differs from
ISOBARIC_ANALYZER, which hard-fails when the matrix path is missing, making the workflow behavior
inconsistent and error-prone.

Agent Prompt

### Issue description
`ISOBARIC_WORKFLOW` silently omits isotope-correction flags when `params.isotope_correction` is true but `params.plex_corr_matrix_file` is null. This produces incorrect (uncorrected) quantification without failing.

### Issue Context
`ISOBARIC_ANALYZER` already enforces the expected contract by erroring when `isotope_correction` is enabled but the matrix file is missing. `ISOBARIC_WORKFLOW` should match that behavior.

### Fix Focus Areas
- modules/local/openms/isobaric_workflow/main.nf[42-58]
- modules/local/openms/isobaric_workflow/main.nf[60-79]
- modules/local/openms/isobaric_analyzer/main.nf[28-35]

### Suggested fix
- If `params.isotope_correction` is true and `params.plex_corr_matrix_file` is null/empty, `error("plex_corr_matrix_file is required when isotope_correction is enabled")`.
- Optionally mirror `ISOBARIC_ANALYZER` and always pass `-quantification:isotope_correction true/false` explicitly for clarity/consistency.

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

[jpfeuffer]

@ypriverol this feels important!