Improving the workflow image

[ypriverol]

Summary by CodeRabbit

Release Notes

• New Features

  • Complete quantmsdiann pipeline infrastructure with DIA-NN data-independent acquisition analysis, spectral library generation, and quantification workflows
  • Multiple pre-configured test profiles for different data acquisition methods
  • Full CI/CD pipeline with automated testing across multiple DIA-NN versions

• Documentation

  • Comprehensive usage and output documentation
  • Contribution guidelines and development workflows
  • Configuration profiles for various execution environments (SLURM, cloud, local)

• Tests

  • Test profiles for standard DIA, DIA-PASEF, QuantUMS, and Parquet-native analyses
  • nf-test framework integration for module and pipeline validation

• Chores

  • GitHub issue and pull request templates
  • Code linting and formatting configuration
  • RO-Crate metadata for workflow provenance

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📝 Walkthrough

Walkthrough

This pull request introduces a complete, production-ready bioinformatics pipeline (bigbio/quantmsdiann) for DIA-NN–based proteomics mass spectrometry data analysis. The addition comprises Nextflow DSL2 workflows, DIA-NN processing modules, multiple test/configuration profiles, comprehensive GitHub Actions CI/CD workflows, parameter schemas, documentation, and supporting assets for a complete from-RAW-to-quantification analysis pipeline.

Changes

Cohort / File(s)	Summary
Documentation & Contribution Guidelines README.md, docs/usage.md, docs/output.md, docs/README.md, .github/CONTRIBUTING.md, AGENTS.md, CHANGELOG.md, CITATIONS.md, CODE_OF_CONDUCT.md, .github/skills/sdrf/SKILL.md	Complete user-facing and contributor documentation including pipeline overview, quick-start instructions, output structure, contribution workflow, development guidelines, and software citations.
GitHub Issue Templates & Configuration .github/ISSUE_TEMPLATE/bug_report.yml, .github/ISSUE_TEMPLATE/feature_request.yml, .github/ISSUE_TEMPLATE/config.yml	Structured issue templates for bug reports and feature requests with contact links to nf-core community and Slack channel.
GitHub Actions Workflows .github/workflows/ci.yml, .github/workflows/extended_ci.yml, .github/workflows/merge_ci.yml, .github/workflows/clean-up.yml, .github/workflows/linting.yml, .github/workflows/linting_comment.yml, .github/workflows/branch.yml, .github/workflows/fix_linting.yml, .github/workflows/template-version-comment.yml	Complete CI/CD pipeline including default/extended test matrices, branch protection, linting, and automated comment workflows for DIA-NN version handling (1.8.1, 2.1.0, 2.2.0).
GitHub Actions & Dockstore Configuration .github/actions/get-shards/action.yml, .github/actions/nf-test/action.yml, .github/.dockstore.yml, .github/PULL_REQUEST_TEMPLATE.md	Composite GitHub Actions for nf-test sharding and execution; Dockstore workflow registry configuration; PR checklist template.
Project Configuration Files .nf-core.yml, modules.json, .gitignore, .gitattributes, .pre-commit-config.yaml, .prettierignore, .prettierrc.yml, nf-test.config, ro-crate-metadata.json	Repository-level metadata, module manifests, code style/linting configuration, nf-test settings, and RO-Crate research object metadata.
Nextflow Configuration & Profiles nextflow.config, conf/base.config, conf/dev.config, conf/wave.config, conf/pride_codon_slurm.config, conf/diann_versions/*.config, conf/modules/*.config	Core Nextflow configuration with default parameters, base resource profiles, DIA-NN container/version overrides, shared module publishDir rules, and institution-specific executor configurations.
Test Profiles Configuration conf/tests/test_dia.config, conf/tests/test_dia_dotd.config, conf/tests/test_dia_2_2_0.config, conf/tests/test_dia_quantums.config, conf/tests/test_dia_parquet.config, conf/tests/test_latest_dia.config, conf/tests/test_full_dia.config	Multiple test configuration profiles covering DIA-NN versions, input formats (mzML, Bruker .d), and feature variants (QuantUMS, Parquet output).
Parameter Schema & Validation nextflow_schema.json, assets/schema_input.json	Comprehensive JSON schemas defining pipeline parameters, input/output constraints, file formats, and validation rules for parameter documentation and runtime validation.
Email & Notification Templates assets/email_template.html, assets/email_template.txt, assets/sendmail_template.txt, assets/slackreport.json, assets/adaptivecard.json, assets/methods_description_template.yml	Email/Slack/Teams notification templates for pipeline completion reporting, success/failure status, and configuration summaries.
MultiQC Configuration & Assets assets/multiqc_config.yml	MultiQC configuration for custom data reporting, plot configuration, and input file mapping for DIA-NN proteomics QC.
Core Workflows main.nf, workflows/quantmsdiann.nf, workflows/dia.nf	Main entry point and orchestration workflows that coordinate input validation, file preparation, DIA-NN analysis stages, and MultiQC report generation.
Subworkflows – Input & File Handling subworkflows/local/input_check/main.nf, subworkflows/local/input_check/meta.yml, subworkflows/local/create_input_channel/main.nf, subworkflows/local/create_input_channel/meta.yml, subworkflows/local/file_preparation/main.nf, subworkflows/local/file_preparation/meta.yml	Input validation, SDRF parsing, and multi-format file preparation (RAW, mzML, Bruker .d decompression, optional indexing) with metadata enrichment.
Subworkflows – Pipeline Utilities subworkflows/local/utils_nfcore_quantms_pipeline/main.nf, subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml, subworkflows/nf-core/utils_nextflow_pipeline/main.nf, subworkflows/nf-core/utils_nfcore_pipeline/main.nf, subworkflows/nf-core/utils_nfschema_plugin/main.nf, subworkflows/nf-core/utils_nfcore_pipeline/tests/*, subworkflows/nf-core/utils_nextflow_pipeline/tests/*, subworkflows/nf-core/utils_nfschema_plugin/tests/*	Standard nf-core utility workflows for pipeline lifecycle (version/parameter handling, configuration validation, email/webhook notifications, schema-based parameter validation).
DIA-NN Processing Modules modules/local/diann/generate_cfg/main.nf, modules/local/diann/insilico_library_generation/main.nf, modules/local/diann/preliminary_analysis/main.nf, modules/local/diann/assemble_empirical_library/main.nf, modules/local/diann/individual_analysis/main.nf, modules/local/diann/final_quantification/main.nf, modules/local/diann/diann_msstats/main.nf	Individual DIA-NN process modules implementing config generation, in-silico library prediction, preliminary/individual/final analysis stages, empirical library assembly, and MSstats format conversion.
OpenMS & Spectrum Preprocessing Modules modules/local/openms/mzml_indexing/main.nf, modules/local/openms/mzml_indexing/meta.yml, modules/local/utils/mzml_statistics/main.nf, modules/local/utils/mzml_statistics/meta.yml	mzML indexing and spectrum statistics generation modules.
Utility Modules modules/local/utils/decompress_dotd/main.nf, modules/local/utils/decompress_dotd/meta.yml, modules/local/utils/tdf2mzml/main.nf, modules/local/utils/tdf2mzml/meta.yml, modules/local/samplesheet_check/main.nf, modules/local/samplesheet_check/meta.yml, modules/local/sdrf_parsing/main.nf, modules/local/sdrf_parsing/meta.yml, modules/local/pmultiqc/main.nf, modules/local/pmultiqc/meta.yml	Utility modules for format conversion (Bruker TDF to mzML), archive decompression, sample sheet validation, SDRF parsing, and QC report aggregation.
BioBB & nf-core Modules modules/bigbio/thermorawfileparser/main.nf, modules/bigbio/thermorawfileparser/meta.yml, modules/bigbio/thermorawfileparser/environment.yml, modules/bigbio/thermorawfileparser/tests/main.nf.test, modules/bigbio/thermorawfileparser/tests/nextflow.config, modules/nf-core/multiqc/main.nf, modules/nf-core/multiqc/meta.yml, modules/nf-core/multiqc/environment.yml, modules/nf-core/multiqc/tests/main.nf.test, modules/nf-core/multiqc/tests/custom_prefix.config, modules/nf-core/multiqc/tests/nextflow.config	Imported modules from bioBB (ThermoRawFileParser for RAW-to-mzML conversion) and nf-core (MultiQC) with metadata, environments, and unit tests.
Module & Subworkflow Metadata modules/local/diann/*/meta.yml, modules/local/openms/*/meta.yml, modules/local/utils/*/meta.yml, subworkflows/local/*/meta.yml, subworkflows/nf-core/*/meta.yml	Metadata definitions for all modules and subworkflows describing inputs, outputs, tool dependencies, and authors.
Pipeline Tests tests/default.nf.test, tests/nextflow.config, tests/.nftignore	End-to-end integration test configuration for the complete pipeline, test data references, and ignored artifact patterns.
Action Plans & Roadmap .claude/actions_plans.md	Documentation of completed Phase 1 development (CI matrix, module cleanup, testing strategy) and future roadmap for DIA-NN 2.x and performance enhancements.
License LICENSE	Updated copyright line from "BigBio Stack" to "The bigbio/quantmsdiann team".

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Main as main.nf
    participant InputCheck as INPUT_CHECK
    participant FilePrep as FILE_PREPARATION
    participant CreateChannel as CREATE_INPUT_CHANNEL
    participant DIA as DIA Workflow
    participant PMULTIQC as PMULTIQC
    participant Output as Results Directory

    User->>Main: nextflow run --input sdrf.tsv --database proteins.fa --outdir results
    Main->>InputCheck: Validate SDRF file
    InputCheck-->>Main: Checked SDRF
    Main->>CreateChannel: Parse SDRF & create metadata
    CreateChannel-->>Main: Channel of (meta, file_path) pairs
    Main->>FilePrep: Prepare input files (convert RAW to mzML, decompress .d)
    FilePrep-->>Main: Prepared mzML files with statistics
    Main->>DIA: Run DIA analysis (in-silico lib → preliminary → empirical → individual → final quant)
    DIA->>DIA: Generate config
    DIA->>DIA: In-silico library generation
    DIA->>DIA: Preliminary analysis
    DIA->>DIA: Assemble empirical library
    DIA->>DIA: Individual MS file analysis
    DIA->>DIA: Final quantification & MSstats conversion
    DIA-->>Main: Quantification matrices & reports
    Main->>PMULTIQC: Aggregate QC & generate MultiQC report
    PMULTIQC-->>Main: MultiQC HTML report
    Main->>Output: Write results
    Output-->>User: Pipeline complete

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Estimated code review effort

🎯 5 (Critical) | ⏱️ ~150 minutes

Possibly related PRs

• extract DIA-NN workflow from quantms #11: Directly related PR that implements the same DIA-NN–focused workflows, DIA-NN processing module stages (preliminary_analysis, individual_analysis, final_quantification), and supporting configurations and tests, indicating overlapping code-level foundational work.

Suggested reviewers

• daichengxin

Poem

🐰 A rabbit hops through data streams so bright,
Raw spectra flowing left and right,
DIA-NN's magic weaves them all,
From library to quantums, standing tall!
MultiQC dances at the end—
A pipeline perfect, friend to friend! 🔬✨

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch yasset-refactoring