Refactoring ongoing for quantmsdiann - iteration one Remove MSStats postprocessing

[ypriverol]

This pull request makes significant updates to the CI/CD infrastructure, documentation, and configuration to fully transition the project from quantms to a streamlined, DIA-NN-only pipeline called quantmsdiann. The changes remove legacy code and tests, introduce a version-aware testing strategy, update documentation, and restructure the extended CI workflow to support feature-specific and version-specific testing.

Key changes include:

CI/CD and Testing Infrastructure

• Overhauled .github/workflows/extended_ci.yml to implement a three-job structure: (1) default tests using public DIA-NN 1.8.1 containers, (2) feature tests using the latest DIA-NN (2.2.0, private containers), and (3) Singularity tests for default profiles. This enables version-aware and feature-specific testing, with improved artifact naming and timestamping. [1] [2] [3] [4]
• Updated .github/workflows/ci.yml to remove non-DIA test profiles and restrict workflow runs to the bigbio/quantmsdiann repository. Only test_dia and test_dia_dotd profiles remain for fast, public CI.
• Removed the obsolete .github/workflows/diann_private.yml workflow, consolidating private container testing into the new extended CI structure.
• Adjusted branch protection workflow and conditions to reference bigbio/quantmsdiann instead of bigbio/quantms.

Documentation and Roadmap

• Added a comprehensive action plan and roadmap in .claude/actions_plans.md, documenting completed cleanup, version-aware testing, and outlining future phases for DIA-NN 2.x support and performance/scalability improvements.
• Updated issue templates and documentation to use the new bigbio/quantmsdiann naming and reflect the DIA-NN-only scope. [1] [2]

Cleanup and Legacy Removal

• Deleted .devcontainer/setup.sh and related devcontainer files, as well as references to legacy quantms artifacts and test profiles, completing the transition to a DIA-NN-only codebase.

These changes collectively modernize the pipeline, improve maintainability, and ensure robust, versioned testing for all DIA-NN features.This pull request focuses on refactoring the pipeline and repository to support a DIA-NN-only workflow under the new bigbio/quantmsdiann name. It removes legacy code and configuration related to non-DIA workflows, updates documentation and CI to reflect the new focus, and introduces a clear roadmap for future development. The changes also update all references, templates, and documentation to use the new pipeline name and branding.

Key changes include:

Pipeline Refactoring and Roadmap

• Added .claude/actions_plans.md with a detailed action plan and roadmap, documenting the completed removal of non-DIA artifacts, and outlining future phases for DIA-NN 2.x support and performance improvements.

Continuous Integration and Testing Updates

• Updated .github/workflows/ci.yml and .github/workflows/extended_ci.yml to remove non-DIA test profiles, restrict CI to the new repository, and add new test profiles relevant to DIA-NN. Also added steps for container registry authentication. [1] [2] [3] [4] [5]
• Removed the fork-specific CI workflow .github/workflows/diann_private.yml, as it is no longer relevant for the new pipeline.
• Updated branch protection workflow to check for pull requests in the bigbio/quantmsdiann repository instead of the old one.

Documentation and Branding

• Overhauled README.md with a new pipeline overview, workflow diagram, supported formats, quick start instructions, and updated credits/citation for quantmsdiann.
• Updated email templates and other documentation to consistently refer to bigbio/quantmsdiann instead of bigbio/quantms. [1] [2] [3]
• Updated issue templates to reference the new pipeline name. [1] [2]

Cleanup and Licensing

• Removed the .devcontainer/setup.sh script, cleaning up unused development container setup code.
• Updated LICENSE to reflect the new team ownership.

Changelog and Minor Edits

• Minor formatting and header updates in CHANGELOG.md.

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[Copilot]

Pull request overview

This PR refactors the pipeline into a DIA-NN–focused bigbio/quantmsdiann workflow by removing non-DIA functionality (e.g., MSstats post-processing, peak picking, DDA/TMT-related remnants) and updating branding/docs/CI to match the DIA-only scope.

Changes:

• Simplifies the main workflow and DIA subworkflow by removing MSstats post-processing and other non-DIA modules/params.
• Makes input handling explicitly DIA-only (SDRF parsing + DIA acquisition validation) and updates documentation/RO-Crate metadata accordingly.
• Expands CI/testing to cover multiple DIA-NN versions and feature matrices; adds diann_no_peptidoforms support across DIA-NN steps.

Reviewed changes

Copilot reviewed 53 out of 69 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
workflows/quantmsdiann.nf	Removes decoy-db logic; adds minimal DB validation; updates MultiQC logo path
workflows/dia.nf	Removes MSstats LFQ post-processing; clarifies MSstats conversion step
subworkflows/local/utils_nfcore_quantms_pipeline/main.nf	Updates tool citation/bibliography to DIA-only toolset
subworkflows/local/file_preparation/main.nf	Removes OpenMS peak picking integration
subworkflows/local/create_input_channel/meta.yml	Updates subworkflow interface/docs to DIA-only SDRF input/output
subworkflows/local/create_input_channel/main.nf	Enforces DIA acquisition; simplifies channel emission to DIA-only
ro-crate-metadata.json	Rewrites embedded description to quantmsdiann-focused README-like text
README.md	Replaces short description with full DIA-only README + workflow diagram
nextflow.config	Removes unused params; adds new test profiles and DIA-NN version override profiles; updates manifest name/description
nextflow_schema.json	Removes obsolete params/sections; adds diann_no_peptidoforms
modules/local/openms/openms_peak_picker/meta.yml	Removed OpenMS peak picker module metadata
modules/local/openms/openms_peak_picker/main.nf	Removed OpenMS peak picker process
modules/local/msstats/msstats_lfq/meta.yml	Removed MSstats LFQ module metadata
modules/local/msstats/msstats_lfq/main.nf	Removed MSstats LFQ process
modules/local/diann/preliminary_analysis/main.nf	Adds --no-peptidoforms flag wiring
modules/local/diann/insilico_library_generation/main.nf	Adds --no-peptidoforms flag wiring
modules/local/diann/individual_analysis/main.nf	Adds --no-peptidoforms flag wiring
modules/local/diann/final_quantification/main.nf	Adds --no-peptidoforms flag wiring
modules/local/diann/assemble_empirical_library/main.nf	Adds --no-peptidoforms flag wiring
modules.json	Renames pipeline metadata to bigbio/quantmsdiann; removes unused module entries
LICENSE	Updates copyright holder text (license remains MIT)
docs/usage.md	Rewrites usage docs for bigbio/quantmsdiann and DIA-only operation
docs/README.md	Adds docs index page
docs/output.md	Rewrites output docs for DIA-only outputs/structure
docs/images/quantmsdiann_workflow.svg	Adds new DIA-only workflow diagram
docs/images/nf-core-quantmsdiann_logo_light.png	Adds new docs logo (light)
docs/images/nf-core-quantmsdiann_logo_dark.png	Adds new docs logo (dark)
docs/images/id_pipeline.svg	Removes legacy ID pipeline diagram
conf/tests/test_latest_dia.config	Updates “latest” test to DIA-NN 2.2.0 container
conf/tests/test_dia.config	Removes MSstats post-processing param from DIA test
conf/tests/test_dia_quantums.config	Adds QuantUMS feature test profile
conf/tests/test_dia_parquet.config	Adds Parquet/decoy-report feature test profile
conf/tests/test_dia_dotd.config	Removes MSstats post-processing param from .d test
conf/tests/test_dia_2_2_0.config	Adds explicit DIA-NN 2.2.0 compatibility test profile
conf/pride_codon_slurm.config	Removes resource overrides for removed PROTEOMICSLFQ process
conf/modules/verbose_modules.config	Cleans verbose publishDir rules to DIA-only structure
conf/modules/shared.config	Removes MSstats publish rules; restricts quant table publishing to DIA-NN steps
conf/diann_versions/v2_2_0.config	Adds CI override profile for DIA-NN 2.2.0 container
conf/diann_versions/v2_1_0.config	Adds CI override profile for DIA-NN 2.1.0 container
conf/diann_versions/v1_8_1.config	Adds CI override profile for DIA-NN 1.8.1 container
conf/dev.config	Removes unused container override for removed ONSITE step
CITATIONS.md	Prunes citations to DIA-only toolchain; updates pipeline name header
CHANGELOG.md	Minor formatting cleanup
bin/msstats_plfq.R	Removes legacy MSstats R script
assets/sendmail_template.txt	Updates embedded logo name/path references
assets/email_template.txt	Updates pipeline name/URLs in email text template
assets/email_template.html	Updates pipeline name/description/URLs in HTML email template
assets/nf-core-quantmsdiann_logo_light.png	Adds new pipeline logo asset
.nf-core.yml	Adds .gitignore to lint inputs
.gitignore	Replaces large Python-oriented ignore list with Nextflow/pipeline-focused ignores
.github/workflows/merge_ci.yml	Adds merge CI workflow with version × feature testing matrix
.github/workflows/extended_ci.yml	Refactors extended CI into staged jobs (default → latest → singularity) for DIA-only tests
.github/workflows/ci.yml	Restricts CI matrix to DIA-only test profiles and repo name
.github/workflows/branch.yml	Updates branch protection logic to bigbio/quantmsdiann
.github/workflows/diann_private.yml	Removes fork-specific workflow for private container testing
.github/ISSUE_TEMPLATE/feature_request.yml	Updates pipeline name in template description
.github/ISSUE_TEMPLATE/bug_report.yml	Updates pipeline name in template prompt
.devcontainer/setup.sh	Removes devcontainer setup script
.claude/actions_plans.md	Adds internal roadmap/action plan doc for the refactor

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