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Co-authored-by: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Co-authored-by: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Removed redundant paragraph
Update for README.md
preparing for version 1.4.1dev
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Adding met-excision as parameter to DIA and DDA workflows
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Pull Request Overview
This PR prepares the 1.5.0 release by bumping the version, refining documentation, and adding new test flags.
- Bump pipeline version to 1.5.0 and update CHANGELOG, README, and .nf-core.yml.
- Enhance
docs/output.mdwith detailed default output structure and pMultiQC references. - Introduce new parameters (
mzml_features,add_snr_feature_percolator) in test configs and add DSL2 module configs underconf/modules.
Reviewed Changes
Copilot reviewed 132 out of 132 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/output.md | Clarify output directories, fix pMultiQC references |
| README.md | Remove outdated snippet and add new contributor entry |
| CHANGELOG.md | Add 1.5.0 section with added, changed, fixed, dependencies |
| .nf-core.yml | Update lint/files_unchanged entries and bump version |
| conf/tests/test_lfq.config | Enable mzml_features flag in LFQ test configuration |
| conf/tests/test_dda_id.config | Enable add_snr_feature_percolator in DDA-ID test config |
| conf/modules/verbose_modules.config | Add verbose publishDir overrides for intermediate outputs |
| conf/modules/modules.config | Define default DSL2 per-module publishDir options |
Comments suppressed due to low confidence (3)
conf/tests/test_lfq.config:38
- [nitpick] Add or update unit/integration tests to cover the new 'mzml_features' flag and verify expected behavior when enabled.
mzml_features = true
conf/tests/test_dda_id.config:39
- [nitpick] Include tests to confirm that enabling 'add_snr_feature_percolator' actually triggers SNR feature addition in the Percolator step.
add_snr_feature_percolator = true
README.md:160
- Remove the stray empty code block delimiters at the end of the README to avoid rendering an unintended blank code section.
</details>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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♻️ Duplicate comments (1)
docs/output.md (1)
28-28: Add missing comma after "pMultiQC"Improve readability by adding a comma:
- Generation of QC reports using pMultiQC a library for QC proteomics data analysis. + Generation of QC reports using pMultiQC, a library for QC proteomics data analysis.
🧹 Nitpick comments (1)
docs/output.md (1)
5-5: Use consistent English spellingThis file currently mixes British English ("summarises", "visualisation") with American English ("visualizations"). Select one variant and apply it consistently across documentation.
Also applies to: 37-37
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🔇 Additional comments (6)
docs/output.md (6)
16-21: Clear addition of LC-MS predictor and rescoring stepsThe newly added steps 4–9 clearly describe LC-MS feature prediction, SNR feature addition, merging runs, PSM rescoring, and FDR combination. The documentation aligns with the pipeline enhancements.
30-30: Grammar fix applied correctlyThe phrase "For DIA-LFQ experiments, the workflow is different:" correctly resolves the prior grammar issue.
33-33: Grammar fix applied correctlyThe line "DIA-NN is used for identification and quantification…" now reads clearly and fixes the earlier typo.
43-43: Clarify output directory descriptionThe sentence explaining
--outdirand standard file formats is concise and informative, helping users understand where and how outputs are organized.
45-46: mzML and mzTab definitions are accurateThe links and descriptions for mzML and mzTab are correct, using valid URLs and clarifying the formats.
368-368: pMultiQC usage description is clearThe note on pMultiQC report collation and the link to the repository provide valuable context and traceability.
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Pull Request Overview
This release updates the pipeline to version 1.5.0, standardizes output documentation and directory layouts, adds new test flags, and restructures module configuration (including a verbose-mode config).
- Update output docs to reflect pMultiQC plugin and detailed directory structures
- Add new parameters (
mzml_features,add_snr_feature_percolator) to test configs - Replace old
conf/modules.configwith a modularconf/modules/modules.configand addconf/modules/verbose_modules.config
Reviewed Changes
Copilot reviewed 132 out of 132 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| docs/output.md | Updated output documentation for pMultiQC reports and default/verbose structures |
| conf/tests/test_lfq.config | Added mzml_features = true to exercise new features |
| conf/tests/test_dda_id.config | Enabled SNR feature for Percolator rescore |
| conf/modules/verbose_modules.config | New verbose-mode publishDir overrides for intermediate files |
| conf/modules/modules.config | Modularized publish rules and conditional blocks |
| conf/modules.config | Removed legacy top-level modules config |
| conf/igenomes_ignored.config | Removed legacy iGenomes stub config |
| README.md | Incorporated new contributor and cleaned up duplicates |
| CHANGELOG.md | Added 1.5.0 changelog entries |
| .nf-core.yml | Bumped pipeline version; updated lint file list |
Comments suppressed due to low confidence (2)
.nf-core.yml:11
- The lint section still references
conf/modules.configandconf/igenomes_ignored.configeven though those files were removed. Please remove or update these entries to avoid CI failures.
- - conf/modules.config
docs/output.md:56
- [nitpick] Indentation of nested list items under
pmultiqc/is inconsistent; aligning bullets by two spaces (or using proper markdown nesting) will improve readability.
- `pmultiqc/`: Contains pMultiQC reports and visualizations
There was a problem hiding this comment.
Pull Request Overview
This PR updates the pipeline to version 1.5.0, adds new parameters and modules configurations, and refreshes documentation and CI lint settings.
- Bumps version to 1.5.0 and updates CHANGELOG, README, and .nf-core.yml.
- Adds
mzml_featuresandadd_snr_feature_percolatorto test configs. - Introduces new
conf/modules/verbose_modules.configandconf/modules/modules.config, removes outdated configs, and extends output documentation.
Reviewed Changes
Copilot reviewed 132 out of 132 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/output.md | Updated output docs for pMultiQC, default/verbose directory structure. |
| conf/tests/test_lfq.config | Enabled new mzml_features parameter. |
| conf/tests/test_dda_id.config | Added add_snr_feature_percolator parameter. |
| conf/modules/verbose_modules.config | Added verbose publishDir mappings for intermediate steps. |
| conf/modules/modules.config | Introduced central modules config with publishDir rules and conditions. |
| conf/modules.config | Removed outdated modules.config file. |
| conf/igenomes_ignored.config | Removed unused iGenomes ignore config. |
| README.md | Removed duplicate intro paragraph; added new contributor. |
| CHANGELOG.md | Updated to v1.5.0 and listed added, changed, fixed items. |
| .nf-core.yml | Updated lint patterns, removed old modules config entries, bumped version. |
Comments suppressed due to low confidence (3)
conf/tests/test_lfq.config:38
- Added new parameter
mzml_features, but there is no test validating its effect on output directory structure or process activation; consider adding assertions or coverage for modules that depend on this parameter.
mzml_features = true
conf/tests/test_dda_id.config:39
- Introduced
add_snr_feature_percolatorparameter; ensure there are tests verifying that SNR features are correctly included in Percolator rescoring outputs.
add_snr_feature_percolator = true
.nf-core.yml:20
- Duplicate entry for
conf/modules.configin lint file lists; consider removing redundant lines to avoid confusion in CI linting patterns.
- - conf/modules.config
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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♻️ Duplicate comments (1)
docs/output.md (1)
28-28: Comma needed after pMultiQC
Insert a comma for correct apposition: “pMultiQC, a library…”- 16. Generation of QC reports using pMultiQC a library for QC proteomics data analysis. + 16. Generation of QC reports using pMultiQC, a library for QC proteomics data analysis.
🧹 Nitpick comments (5)
docs/output.md (5)
5-5: Link pMultiQC in introduction
Add a hyperlink to the pMultiQC plugin to aid discoverability.- This document describes the output produced by the pipeline. Most plots are taken from the pMultiQC report, which summarises results at the end of the pipeline. + This document describes the output produced by the pipeline. Most plots are taken from the [pMultiQC](https://github.com/bigbio/pmultiqc) report, which summarises results at the end of the pipeline.
16-18: Unify list item verb forms for consistency
Standardize the pipeline step descriptions to use parallel gerund forms and clearer phrasing.- 4. (optional) Performs LC-MS predictors such as MS²PIP and DeepLC to add new peptide spectrum match (PSM) features by MS2Rescore - 5. (optional) Add spectrum signal-to-noise (SNR) features for Percolator rescore - 6. (optional) Merge different MS runs by samples or whole projects + 4. (optional) Perform LC-MS predictions (MS²PIP, DeepLC) to add PSM features via MS2Rescore + 5. (optional) Add spectrum signal-to-noise (SNR) features via Percolator rescore + 6. (optional) Merge multiple MS runs by sample or project
33-33: Remove unnecessary article “the”
Simplify phrasing by dropping the definite article before plural objects.- 2. DIA-NN is used for identification and quantification of the peptides and proteins + 2. DIA-NN is used for identification and quantification of peptides and proteins
43-43: Refine--outdirdescription
Use more natural wording and move backticks to the parameter name.- Output will be saved to the folder defined by the parameter `--outdir`. Each step of the workflow exports different files and reports with the specific data, peptide identifications, protein quantifications, etc. Most of the pipeline outputs are [HUPO-PSI](https://www.psidev.info/) standard file formats: + Output will be saved in the folder specified by the `--outdir` parameter. Each step of the workflow exports files and reports containing specific data (peptide identifications, protein quantifications, etc.). Most outputs follow the [HUPO-PSI](https://www.psidev.info/) standard file formats:
368-368: Hyperlink the GitHub URL
Convert the raw URL to a markdown link for consistency.- For more information about how to use pMultiQC reports in general, see <https://github.com/bigbio/pmultiqc>. + For more information about how to use pMultiQC reports in general, see [pMultiQC](https://github.com/bigbio/pmultiqc).
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🔇 Additional comments (1)
docs/output.md (1)
45-46: Corrected mzTab link
The mzTab URL is now correct and Markdown syntax is valid.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).Summary by CodeRabbit
New Features
Improvements
Bug Fixes
Documentation
Style/Refactor
Chores