support pmultiqc 0.0.31

[yueqixuan]

User description

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the bigbio/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

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PR Type

Enhancement

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Description

• Update pmultiqc container version from 0.0.28 to 0.0.30

• Modify multiqc configuration for new pmultiqc version

• Add support for diann_report_parquet output format

• Disable plot exports in multiqc configuration

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Diagram Walkthrough

flowchart LR
  A["pmultiqc 0.0.28"] --> B["pmultiqc 0.0.30"]
  B --> C["Updated Configuration"]
  C --> D["New Parquet Support"]
  C --> E["Disabled Plot Exports"]

Loading

File Walkthrough

	Relevant files
Configuration changes	multiqc_config.yml Update multiqc configuration for pmultiqc 0.0.30                  assets/multiqc_config.yml Change export_plots from true to false Update sp section prefixes from quantms/ to pmultiqc/ Add new pmultiqc/diann_report_parquet configuration Rename diann_report to diann_report_tsv +12/-9
Dependencies	main.nf Upgrade pmultiqc container to version 0.0.30                          modules/local/pmultiqc/main.nf Update container version from 0.0.28 to 0.0.30 Remove optional plots output channel +2/-3
Enhancement	dia.nf Add parquet report output support                                                workflows/dia.nf Add diann_report_parquet to emit outputs Include FINAL_QUANTIFICATION.out.report_parquet in outputs +7/-6      quantms.nf Switch to parquet format for DIA results                                  workflows/quantms.nf Replace DIA.out.final_result with DIA.out.diann_report_parquet Update pipeline results mixing for new parquet format +1/-1

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[qodo-code-review]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Logic Change The replacement of DIA.out.final_result with DIA.out.diann_report_parquet changes the pipeline output behavior. Need to verify this substitution is intentional and doesn't break downstream processing that might expect the original final_result format. ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report_parquet) ch_msstats_in = ch_msstats_in.mix(DIA.out.msstats_in) Missing Output The removal of the optional plots output channel may break existing workflows or scripts that depend on plot generation. Verify this removal aligns with the disabled plot exports configuration. output: path "*.html", emit: ch_pmultiqc_report path "*.db", optional: true, emit: ch_pmultiqc_db path "versions.yml", emit: versions path "*_data", emit: data

[qodo-code-review]

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