First release of quantmsdiann including new features previously no supported by ypriverol · Pull Request #27 · bigbio/quantmsdiann

ypriverol · 2026-04-01T15:54:42Z

This pull request introduces foundational project management and contribution infrastructure for the bigbio/quantmsdiann pipeline. It adds comprehensive documentation for contributors, issue and PR templates, CI/CD and Dockstore configuration, and a detailed action plan and roadmap for the pipeline's development. These changes are essential for establishing best practices, improving collaboration, and guiding future development.

The most important changes are:

Project Management & Documentation

Added a detailed action plan and roadmap for the quantmsdiann pipeline, outlining completed and planned phases, version-aware testing strategy, and a decision log in .claude/actions_plans.md.
Introduced comprehensive contributing guidelines in .github/CONTRIBUTING.md, covering workflow, testing, patching, conventions, and Codespaces support.

Issue and PR Templates

Added GitHub issue templates for bug reports, feature requests, and contact links, as well as a pull request template to standardize contributions and reviews. [1] [2] [3] [4]

CI/CD and Tooling Configuration

Added Dockstore configuration for workflow publishing in .github/.dockstore.yml.
Added a composite GitHub Action (.github/actions/get-shards/action.yml) to dynamically determine the number of test shards for CI jobs based on changed files and tags.

Repository Metadata

Updated .gitattributes to improve linguist language detection and mark nf-core generated files.

Summary by CodeRabbit

New Features
- Complete DIA-NN-based proteomics pipeline with support for multiple data formats (.raw, .mzML, Bruker .d files)
- Flexible DIA-NN version management (1.8.1, 2.1.0, 2.2.0)
- Comprehensive quality control and reporting via pmultiqc
- MSstats-compatible quantification outputs
- Full pipeline documentation and contribution guidelines
Documentation
- Added usage guide, output format documentation, and API guidelines
- Established Code of Conduct and contribution workflow

extract DIA-NN workflow from quantms

Add Peptidoform Scoring Control

…sdiann into yasset-refactoring

small changes

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- ch_diann_cfg is already a single-emission channel from SDRF_PARSING, .first() was causing a Nextflow warning about useless operator on value channels - Remove stale TODO comments about ch_versions naming and nf-validation Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

DIA-NN 1.8.1 doesn't recognize --direct-quant (introduced with QuantUMS in 1.9.2). Direct quantification is the default in 1.8.1, so the flag is unnecessary. Now only passed when version >= 1.9. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Add DIA-NN 2.3.2 to version selection table in usage.md - Document version-dependent features (QuantUMS >= 1.9.2, DDA >= 2.3.2, InfinDIA >= 2.3.0) with automatic compatibility handling - Fix parameters.md: QuantUMS description now correctly explains --direct-quant behavior and version requirements Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

modules/local/parse_empirical_log_task/main.nf

jpfeuffer · 2026-04-05T12:05:21Z

I think the number one priority for this should now be to not convert hundreds of gigabytes of .d to mzml just for a bit of qc. Do we even need indexed mzml for QC or why do you have the indexing step? Use the new .d reading capabilities of pyopenms if they are sufficient, otherwise there are many other libraries that can read .d these days.

workflows/quantmsdiann.nf

- .nf-core.yml: set is_nfcore to false, remove non-existent files from lint exclusions (conf/test.config, conf/test_full.config, conf/modules.config, conf/igenomes_ignored.config) - .dockstore.yml: use uppercase NFL for Dockstore subclass - SKILL.md: fix default output format from csv to tsv for SDRF - pmultiqc/meta.yml: align inputs/outputs with actual process definition - sdrf_parsing/main.nf: use idiomatic .name instead of .Name - parse_empirical_log_task: run on head node (executor local) instead of spawning a compute node for simple log grep - CI actions: remove unused paths input from nf-test and get-shards Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Remove the convert_dotd parameter and TDF2MZML module. DIA-NN handles Bruker .d files natively, so converting hundreds of GB to mzML just for QC statistics is wasteful (per jpfeuffer's review). Native .d QC support will be tracked in a separate issue. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Replace script+executor local with an exec block that runs Groovy code directly on the head node. This is the idiomatic Nextflow approach for lightweight tasks — no container, no compute node, no scheduler overhead. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Remove unused logo

Per jpfeuffer's review: users who skip preliminary analysis already know their mass accuracy and scan window parameters — no need to pass a log file. For the normal workflow, parse calibrated values directly inside ASSEMBLE_EMPIRICAL_LIBRARY (same node, zero overhead) instead of spawning a separate process. Removes: PARSE_EMPIRICAL_LOG subworkflow, PARSE_EMPIRICAL_LOG_TASK module, and --empirical_assembly_log parameter. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The database parameter is already declared as required with exists validation in nextflow_schema.json — nf-schema enforces this before the workflow starts. Per daichengxin's review. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Add conf/modules.config, conf/test.config, conf/test_full.config, conf/igenomes.config, and conf/igenomes_ignored.config back to files_exist ignore list. Add .dockstore.yml to files_unchanged to suppress template mismatch from NFL uppercase fix. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The env output directive fails at Nextflow compilation. Switch to writing calibrated_params.txt and reading it via .map { f.text }. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Instead of writing a file or using env output, parse the calibrated mass accuracy and scan window values directly from the assembly log using a .map operation in the workflow. This runs as Groovy on the head node with zero overhead — no extra process, no extra file. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Pull request overview

Copilot reviewed 131 out of 136 changed files in this pull request and generated 11 comments.

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workflows/quantmsdiann.nf

workflows/dia.nf

subworkflows/local/file_preparation/main.nf

subworkflows/local/create_input_channel/main.nf

modules/bigbio/thermorawfileparser/main.nf

conf/wave.config

workflows/dia.nf

Remove non-existent files from .nf-core.yml lint checks, remove phantom quantms_log input from pmultiqc meta.yml, fix tdf2mzml input description, and add missing ms2_statistics/feature_statistics outputs to file_preparation. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The files_exist list excludes files from the lint existence check. Re-add nf-test.yml, modules.config, test.config, and test_full.config so nf-core lint skips checking for them. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Update pipeline name in config comments, nextflow run examples, module homepages, ro-crate metadata, version output filename, and custom config path to consistently use bigbio/quantmsdiann. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

The quantmsdiann.config does not exist in nf-core/configs yet, causing nextflow config to fail with a file-not-found error during linting. Remove the include until a pipeline-specific config is submitted. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Reuse the existing quantms institutional profiles from nf-core/configs since quantmsdiann shares the same infrastructure requirements. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

yueqixuan and others added 30 commits March 14, 2026 18:48

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Merge pull request #11 from yueqixuan/dev

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extract DIA-NN workflow from quantms

Refactoring ongoing for quantmsdiann

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remove some unnecesary files

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minor changes

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minor changes in pre-commit

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add diann_no_peptidoforms

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minor changes in the CI/CD

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Merge pull request #13 from yueqixuan/yasset-refactoring

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Add Peptidoform Scoring Control

Resstructured

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Merge branch 'yasset-refactoring' of https://github.com/bigbio/quantm…

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…sdiann into yasset-refactoring

minor changes AGENTS.md

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Minor changes in AGENTS.md

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minor changes in the gitignore

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improve in the CI/CD and more cleanning

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minor changes in CI/CD to know the DIANN version

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README updated

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minor change in the README

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Minor changes to README.md

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small changes

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minor changes from code review

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Merge pull request #14 from yueqixuan/yasset-refactoring

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ypriverol and others added 4 commits April 5, 2026 07:37

docs: add parameters link to docs/README.md

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Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

jpfeuffer reviewed Apr 5, 2026

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daichengxin approved these changes Apr 5, 2026

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yueqixuan and others added 4 commits April 5, 2026 21:00

Remove unused logo

085cbb0

Remove unused logo

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ypriverol mentioned this pull request Apr 5, 2026

Add native Bruker .d file support for QC statistics #34

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3 tasks

ypriverol and others added 8 commits April 5, 2026 16:30

Merge pull request #33 from yueqixuan/dev

dd3dfbb

Remove unused logo

style: fix prettier formatting in parameters.md

6fd5b0a

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

fix: use file output instead of env for calibrated params

2d0e2fa

The env output directive fails at Nextflow compilation. Switch to writing calibrated_params.txt and reading it via .map { f.text }. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ypriverol requested a review from Copilot April 5, 2026 19:36

Copilot started reviewing on behalf of ypriverol April 5, 2026 19:36 View session

Copilot AI reviewed Apr 5, 2026

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ypriverol and others added 5 commits April 6, 2026 06:56

fix: restore pipeline config include pointing to quantms.config

25871fb

Reuse the existing quantms institutional profiles from nf-core/configs since quantmsdiann shares the same infrastructure requirements. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ypriverol merged commit 876342a into main Apr 6, 2026
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coderabbitai bot mentioned this pull request Apr 6, 2026

Small patch to fix release CI/CD tests #35

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First release of quantmsdiann including new features previously no supported#27

First release of quantmsdiann including new features previously no supported#27
ypriverol merged 127 commits intomainfrom
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ypriverol commented Apr 1, 2026 •

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ypriverol commented Apr 1, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Pull request overview

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ypriverol commented Apr 1, 2026 •

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