[Shen-YuFei]

Summary

Fixes found while re-analysing public spike-in datasets with quantms.

Search modifications from SDRF

• Allow an empty fixed-modification set from SDRF without adding a default modification.
• Trim the selected variable-modification value before validation.
• Reject MS-GF+ searches when both modification sets are empty, because OpenMS MSGFPlusAdapter would otherwise enable fixed Carbamidomethyl (C).

Comet fragment binning

• New optional Comet settings: --comet_fragment_bin_tol (native full width in Da), --comet_fragment_bin_offset and --comet_instrument. Per-run overrides are available through ext.comet_fragment_bin_tol, ext.comet_fragment_bin_offset and ext.comet_instrument. The width is divided by two for OpenMS CometAdapter.
• Without these settings, the automatic behaviour is kept. Da tolerances use the same adapter tolerance, offset and instrument mode as before. ppm tolerances use the previous guess (below 50 ppm: 0.03 Da bin, offset 0, high_res; otherwise 1.0005 Da, offset 0.4, low_res) and log a warning.
• The effective settings are written to .nextflow.log at DEBUG level.

MS2 rescoring tolerance

• MSRESCORE_FEATURES passes the SDRF fragment tolerance value and unit (Da or ppm) unchanged. The configured fallback is used only when both fields are absent.
• The rescoring modules use quantms-rescoring 0.0.25, which includes MS2PIP 4.2 with ppm support (Fix multi-engine identification indices and index= spectrum references; support unit-aware MS2PIP 4.2 quantms-rescoring#99). They move to the next release once fix(idparquet): Keep one identification per spectrum when merging search engines quantms-rescoring#102 is released (see below).

Sage

• Match each split identification file to its run by exact name. Before, the glob fr1*_sage.idparquet also matched fr10 (seen in PXD011691).
• Declare Sage outputs for Bruker .d runs without the .d suffix, as IDRipper names them.

Independent LFQ groups (--lfq_group_by)

• New optional parameter. It names SDRF columns; each combination of values is quantified by its own ProteomicsLFQ run, with its own OpenMS design, SDRF and QPX output (qpx/<group>.sdrf/).
• All runs are kept. A fractionated sample cannot cross groups. Missing runs or conflicting assignments are errors.
• The local patch of bigbio/qpx/openmsconsensus (tuple input [consensusXML, SDRF] and task.ext.prefix) is recorded in modules.json, regenerated against the qpx 1.1.5 module from chore(qpx): update qpx/openmsconsensus module to qpx 1.1.5 #738.
• PREPARE_LFQ_GROUPS calls quantmsutilsc splitlfqgroups from quantms-utils 0.0.31 (Add splitlfqgroups: split an LFQ design into independent quantification groups by SDRF columns quantms-utils#84). bin/split_lfq_groups.py and its pytest are removed from this repository.
• The group table lfq_groups.tsv is also passed to the pmultiqc report step. feat(qpx): Report cross-run QC per quantms LFQ group pmultiqc#746 uses it to report cross-run QC per group. The current container, pmultiqc 0.0.48, ignores the file; after a pmultiqc release with #746, only the container version needs to change.
• Without --lfq_group_by the output layout is unchanged.

Other

• Make .hooks/block_pipeline_outdir.sh executable, as the pre-commit hook calls it directly.

quantms-rescoring: 0.0.25 and the pending release

When PSM_CLEAN merges several search engines, 0.0.24 could give identifications of different spectra the same index. 0.0.25 indexes each engine's identifications separately, which removes those collisions, but a spectrum found by two engines then becomes two identifications:

• test_lfq: on identical Comet and Sage results, 0.0.24 gives psm 51, feature 41, pg 25, and 0.0.25 gives psm 61, feature 46, pg 23. The 9 PSMs found only with 0.0.24 all had the same PEP (0.047619); of 16 checked spectra found only with 0.0.25, 11 match BSA.
• test_tmt and test_tmt_corr fail in CI. IsobaricWorkflow quantifies each identification, so a spectrum with two identifications is quantified twice, and the QPX export rejects the repeated feature key (ConsensusMapArrowExport: refusing invalid QPX feature batch ... repeats the QPX feature primary key). In test_tmt, 1851 of 5599 spectra were split, and 46 still had two identifications after Percolator.

bigbio/quantms-rescoring#102 keeps one identification per spectrum. Until a release includes it, test_tmt and test_tmt_corr fail on this branch; after the release, the four rescoring modules move to that version. With a container built from quantms-rescoring main plus #102:

• test_tmt: one identification per spectrum after Percolator. Against 0.0.24, target PSMs go from 3166 to 3282 and proteins in the MSstats input from 463 to 477.
• test_lfq: psm 62, feature 46, pg 24.

Verification

Nextflow 26.04.6, Docker.

• pre-commit run --files <changed files>: passed.
• nf-core pipelines lint: 0 failures.
• nf-test (--profile docker): 37 tests passed (Comet binning 17, LFQ grouping 3, qpx/openmsconsensus 1, create_input_channel 16).
• pytest tests/test_sage_outputs.py: 1 passed.
• -profile test_lfq,docker: passed with released containers only. QPX rows: psm 61, feature 46, pg 23.
• -profile test_lfq,docker --lfq_group_by 'source name': passed with released containers (quantms-utils 0.0.31 biocontainer). Three groups, three ProteomicsLFQ tasks, and each QPX dataset contains only the two fractions of its sample. The report step receives lfq_groups.tsv: with pmultiqc 0.0.48 the report data are the same as without it, and pmultiqc from feat(qpx): Report cross-run QC per quantms LFQ group pmultiqc#746, run on the same report inputs, shows one summary row per group.
• -profile test_dda_id_ms2pip,docker with the SDRF's 0.2 Da and with a 20 ppm copy: passed with quantms-rescoring 0.0.25 (MS2PIP 4.2.0). MS2PIP received the tolerance in Da and in ppm.
• Comet with ppm: PXD000001 searched with Comet only at 20 ppm (automatic binning, high_res) gave 2766 PSMs at q < 0.01, compared with 2778 at the SDRF's 0.2 Da.
• All 7 CI profiles (test_lfq, test_tmt, test_tmt_corr, test_localize, test_dda_id_ms2pip, test_dda_id_alphapeptdeep, test_dda_id_fine_tuning) with -profile <test>,docker,dev on Nextflow 25.10.4 and 26.10.2, using the quantms-rescoring container built with [DOC] how to debug #102: passed.
• -profile test_lfq_sage,docker fails at SAMPLESHEET_CHECK (AttributeError: 'float' object has no attribute 'strip' in sdrf-pipelines) on both this branch and current dev. test_lfq runs Sage as well (search_engines = "comet,sage").

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[qodo-code-review]

PR Summary by Qodo

Allow empty SDRF fixed modifications with safe MS-GF+ validation

🐞 Bug fix 🧪 Tests 📝 Documentation ⚙️ Configuration changes 🕐 20-40 Minutes

AI Description

• Preserve empty SDRF fixed-modification sets without injecting Carbamidomethyl.
• Reject MS-GF+ only when fixed and fallback-resolved variable modifications are both empty.
• Add regression coverage, user guidance, changelog notes, and restore hook executability.

Diagram

graph TD
    A["SDRF row"] --> B["Validate fields"] --> C["Normalize fixed"] --> D["Variable fallback"] --> E{"MS-GF+ empty?"}
    E -- "Yes" --> F["Reject search"]
    E -- "No" --> G["Search metadata"]

Loading

High-Level Assessment

The following are alternative approaches to this PR:

1. Patch or upgrade MSGFPlusAdapter

• ➕ Would permit truly modification-free MS-GF+ searches
• ➕ Could remove the pipeline-specific compatibility check
• ➖ Depends on an upstream OpenMS behavior change or maintained patch
• ➖ Introduces dependency and version-compatibility risk

2. Validate inside search-engine modules

• ➕ Would colocate the restriction with the affected MS-GF+ adapter
• ➕ Could isolate engine-specific rules from input parsing
• ➖ Would detect invalid input later in pipeline execution
• ➖ May duplicate validation across downstream module paths

Recommendation: Keep the PR's centralized, post-fallback validation because it fails early and preserves valid empty-fixed inputs for every engine. An upstream MSGFPlusAdapter fix would be preferable long-term, but relying on it now would not protect current OpenMS versions.

Files changed (6) +81 / -5

Bug fix (1) +7 / -4

main.nfPreserve empty fixed modifications and guard MS-GF+ +7/-4

Preserve empty fixed modifications and guard MS-GF+

• Removes FixedModifications from nonempty required-field validation and normalizes absent or whitespace values to an empty string. After variable fallback resolution, rejects MS-GF+ searches only when both modification sets remain empty.

subworkflows/local/create_input_channel/main.nf

Tests (1) +59 / -0

main.nf.testCover SDRF modification normalization and engine safeguards +59/-0

Cover SDRF modification normalization and engine safeguards

• Adds parameterized nf-test cases for empty, missing, whitespace, and populated fixed modifications; variable fallback behavior; modification-free Comet and Sage searches; MS-GF+ rejection; and retained label and enzyme validation.

subworkflows/local/create_input_channel/tests/main.nf.test

Documentation (3) +15 / -1

CHANGELOG.mdRecord empty fixed-modification handling +6/-0

Record empty fixed-modification handling

• Adds an Unreleased fix entry describing supported empty fixed modifications and the MS-GF+ safeguard against implicit Carbamidomethyl.

CHANGELOG.md

usage.mdDocument SDRF modification resolution rules +8/-0

Document SDRF modification resolution rules

• Explains fixed and variable modification sourcing, fallback behavior, and modification-free search support. Documents why fully empty sets are rejected for MS-GF+ but accepted for Comet and Sage.

docs/usage.md

nextflow_schema.jsonClarify SDRF modification requirements in input help +1/-1

Clarify SDRF modification requirements in input help

• Updates schema help text so fixed modifications are no longer presented as nonempty required values. Describes empty-set support and the MS-GF+ compatibility restriction.

nextflow_schema.json

Other (1) +0 / -0

block_pipeline_outdir.shRestore pipeline-output guard executability +0/-0

Restore pipeline-output guard executability

• Restores the executable file mode for the existing commit guard. The script logic is unchanged.

.hooks/block_pipeline_outdir.sh

[qodo-code-review]

Code Review by Qodo

🐞 Bugs (0) 📘 Rule violations (0) 📜 Skill insights (0)

1. Three test cases exceed line limit ✓ Resolved 📘 Rule violation ⚙ Maintainability

Description

The reject MSGF implicit CAM, require label, and require enzyme test maps each place all
fields on one line beyond the 120-character target. Adding another input or assertion attribute to
these regression cases will further obscure which values distinguish each scenario.

Code

subworkflows/local/create_input_channel/tests/main.nf.test[R16-18]

+        [name: 'reject MSGF implicit CAM', fixed: '', variable: '', fallback: '', error: 'Both modification lists are empty'],
+        [name: 'require label', fixed: '', variable: 'Oxidation (M)', label: '', error: 'Missing or empty required SDRF columns'],
+        [name: 'require enzyme', fixed: '', variable: 'Oxidation (M)', enzyme: '', error: 'Missing or empty required SDRF columns'],

Evidence

Compliance rule 10 applies the 120-character target to changed Nextflow and Groovy code. The three
added test definitions each combine enough map fields on one line to exceed that target.

AGENTS.md: Nextflow and Groovy Code Must Follow Project Style
subworkflows/local/create_input_channel/tests/main.nf.test[16-18]

Agent prompt

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

## Issue description
Three newly added test-case definitions avoidably exceed the project's 120-character line-length target.

## Fix Focus Areas
- subworkflows/local/create_input_channel/tests/main.nf.test[16-18]

## Recommended Fix
Expand each long test map across multiple indented lines while preserving every field and expected value.

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

---

2. Validation text exceeds line limit ✓ Resolved 📘 Rule violation ⚙ Maintainability

Description

The new exit call places the entire interpolated validation message on a single line that exceeds
the project's 120-character target. Editing this message requires scanning a dense line, and future
additions can make the validation branch still harder to review.

Code

subworkflows/local/create_input_channel/main.nf[186]

+        exit(1, "ERROR: Both modification lists are empty for '${filestr}', but OpenMS MSGFPlusAdapter would enable fixed Carbamidomethyl (C) in this case. Use Comet or Sage for a search without modifications.")

Evidence

Compliance rule 10 requires changed Nextflow and Groovy code to generally remain within 120
characters and identifies avoidable excess as a failure. The added validation message is written
entirely on one substantially longer line.

AGENTS.md: Nextflow and Groovy Code Must Follow Project Style
subworkflows/local/create_input_channel/main.nf[186-186]

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 MS-GF+ validation message avoidably exceeds the project's 120-character line-length target.

## Fix Focus Areas
- subworkflows/local/create_input_channel/main.nf[186-186]

## Recommended Fix
Build the message from wrapped interpolated and single-quoted string segments, preserving its exact rendered text, and pass the resulting value to `exit`.

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

---

3. Whitespace-only searches reach MS-GF+ ✓ Resolved 🐞 Bug ≡ Correctness

Description

The new guard tests meta.variablemodifications by Groovy truthiness even though the fallback
assigns params.variable_mods without trimming or normalizing it. When fixed modifications are
empty and --variable_mods contains only whitespace, the guard accepts the row and the MS-GF+
command receives that whitespace as a modification token.

Code

subworkflows/local/create_input_channel/main.nf[185]

+    if (params.search_engines.contains('msgf') && !meta.fixedmodifications && !meta.variablemodifications) {

Evidence

The fallback is stored without normalization, while the added guard only checks truthiness; the
schema permits arbitrary strings, and the downstream adapter tokenizes the stored value directly
into command arguments.

subworkflows/local/create_input_channel/main.nf[178-186]
nextflow_schema.json[302-307]
modules/local/openms/msgf/main.nf[90-91]

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 MS-GF+ empty-modification guard treats a whitespace-only `params.variable_mods` value as nonempty, allowing a semantically empty search configuration to reach the adapter.

## Fix Focus Areas
- subworkflows/local/create_input_channel/main.nf[178-186]
- subworkflows/local/create_input_channel/tests/main.nf.test[8-18]

## Recommended Fix
Normalize the selected SDRF or fallback variable-modification value with null-safe string conversion and `trim()`, producing an empty string when appropriate, before applying the MS-GF+ guard. Add a regression case using an empty fixed set and a whitespace-only fallback with MS-GF+ and assert that validation rejects it.

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

---

Context sources

Review mode: ⚖️ Balanced: This changes runtime SDRF validation and MS-GF+ behavior, including fallback ordering and adapter safety, so it carries meaningful correctness risk despite the localized scope.

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[Copilot]

🟡 Changes recommended

Trim or normalize whitespace-only variable modifications and add regression coverage.

Get a fresh assessment by requesting another Copilot review.

Pull request overview

Fixes SDRF handling so empty fixed modifications remain valid while preventing unsafe empty MS-GF+ modification configurations.

Changes:

• Updates modification validation and fallback behavior.
• Adds regression tests and documentation/changelog updates.
• Restores the pipeline-output hook executable bit.

Review note: whitespace-only variable modifications can bypass the MS-GF+ validation and require normalization.

File summaries

File	Summary
subworkflows/local/create_input_channel/tests/main.nf.test	Adds regression coverage for SDRF modifications.
subworkflows/local/create_input_channel/main.nf	Adjusts modification validation and metadata handling.
nextflow_schema.json	Documents updated input behavior.
docs/usage.md	Explains modification handling and MS-GF+ limitations.
CHANGELOG.md	Records the fix.
.hooks/block_pipeline_outdir.sh	Restores the executable bit without logic changes.

Review details

• Files reviewed: 5/6 changed files
• Comments generated: 1
• Review effort level: Lite

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[nikita-a-v]

I encountered the same issue, and this commit appears to fix it for me (at least while using comet search engine). I noticed the PR was closed without being merged, but I couldn’t find an explanation in the thread. Was the fix superseded or intentionally not merged?

[Shen-YuFei]

@nikita-a-v Hi Nikita, I ran into this issue (and a few others) while running quantms on a batch of PXD datasets, so I'm planning to fix all the problems I hit before reopening this PR. It should be done soon.

[qodo-code-review]

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[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ff88f92

+| ✅ 117 tests passed       |+
#| ❔  18 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   7 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/dda_id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
  _
• pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/quantms/quantms/subworkflows/local/id/main.nf: _ ch_software_versions = ch_software_versions.mix(PHOSPHO_SCORING.out.versions.ifEmpty(null))
  _

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: conf/test.config
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: .github/workflows/ci.yml
• files_exist - File is ignored: .github/workflows/download_pipeline.yml
• files_exist - File is ignored: .github/workflows/nf-test.yml
• files_exist - File is ignored: .gitignore
• files_exist - File is ignored: conf/modules.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• nextflow_config - nextflow_config
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/quantms/quantms/.github/workflows/awstest.yml
• multiqc_config - multiqc_config
• modules_config - modules_config
• container_configs - container_configs

❔ Tests fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .nf-core.yml
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/actions/get-shards/action.yml
• files_exist - File found: .github/actions/nf-test/action.yml
• files_exist - File found: .github/workflows/pr-comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-quantms_logo_light.png
• files_exist - File found: docs/CONTRIBUTING.md
• files_exist - File found: docs/images/nf-core-quantms_logo_light.png
• files_exist - File found: docs/images/nf-core-quantms_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-quantms_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowQuantms.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/pr-comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: extended_ci.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.1.0
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 4.1.0
• Run at 2026-10-16 13:56:50

[daichengxin]

When using the quantms-utils container, it is best to move this Python script into the quantms-utils package.

[jpfeuffer]

Can you elaborate on why the auto settings for comet were a problem? Most people do not know what a bin width is for that or how to set it.
.
Independent LFQ groups: Cool feature. How is this reported in QC report, qpx etc?

[Shen-YuFei]

Can you elaborate on why the auto settings for comet were a problem? Most people do not know what a bin width is for that or how to set it. . Independent LFQ groups: Cool feature. How is this reported in QC report, qpx etc?

Thanks @jpfeuffer.

Comet: You are right, this is too strict. The old automatic settings were not a real problem: in all the ppm datasets I re-analysed, I used the same values. I will restore the automatic default and keep the new Comet options as optional overrides.

LFQ groups: each group has its own QPX output (qpx/<group>.sdrf/) and MSstats table, and sdrf/lfq_groups/lfq_groups.tsv shows which run is in which group. The pmultiqc report still shows all groups together.

[jpfeuffer]

Yeah that is better, thank you!

[ypriverol]

@Shen-YuFei What is the split LFQS? Can you explain the problem here.?

[Shen-YuFei]

@Shen-YuFei What is the split LFQS? Can you explain the problem here.?

@ypriverol I had this problem with the following two datasets. Each dataset has parts that cannot be processed together in one ProteomicsLFQ run:

• PXD003472: 24 LTQ Orbitrap Velos runs (fragment tolerance 0.5 Da, 30 and 240 min gradients) and 12 Q Exactive HF runs (20 ppm, 60 and 120 min).
• PXD003841: three sample preparation methods. One uses fixed carbamidomethylation, and the other two use variable modifications.

ProteomicsLFQ combines the identifications from all runs. When the search settings are different, it stops with an error.

--lfq_group_by takes one or more SDRF columns, for example comment[instrument],comment[gradient duration]. Runs with the same values form one group. The search and rescoring still run once for all files. After that, each group has its own ProteomicsLFQ run, design, MSstats table and QPX output. Before this, the only way was to split the SDRF by hand and run quantms once for each group.

[jpfeuffer]

I think it is an interesting feature that I was also thinking about for longer. I wasnt sure how much complexity this adds though.
I think pmultiqc or something would also need to support this to be fully integrated.
Obviously the easier choice would be to split this SDRF into as many SDRFs as needed BEFORE the workflow.

[Shen-YuFei]

I think it is an interesting feature that I was also thinking about for longer. I wasnt sure how much complexity this adds though. I think pmultiqc or something would also need to support this to be fully integrated. Obviously the easier choice would be to split this SDRF into as many SDRFs as needed BEFORE the workflow.

Thanks @jpfeuffer. The added complexity is small: only ProteomicsLFQ and the QPX conversion run once per group. Search, rescoring and the report still run once. Splitting the SDRF beforehand also works, but then each part needs its own pipeline run and report.

You are right about pmultiqc. It still builds the report. I tried it locally: group support adds about 180 lines to pmultiqc, mostly in the QPX module, plus tests, and quantms only needs to pass the group table it already writes to the report step. The summary counts and the cross-run comparisons (PCA, heatmap, intensity SD) are then computed per group; the per-run sections do not change.