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Add developer guidelines and CLAUDE.md#2144

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FriederikeHanssen merged 11 commits into
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feat/developer-guidelines
Feb 27, 2026
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Add developer guidelines and CLAUDE.md#2144
FriederikeHanssen merged 11 commits into
devfrom
feat/developer-guidelines

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@FriederikeHanssen FriederikeHanssen commented Feb 20, 2026 •
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Closes: #2107

Summary

  • Add docs/DEVELOPER_GUIDELINES.md — comprehensive reference for contributing to sarek, covering code style (Harshil alignment, strict syntax, topic channels), channel operations, meta map handling, module/subworkflow patterns, configuration, testing, documentation requirements, and PR checklist
  • Add CLAUDE.md at repo root pointing to the guidelines, plus agent-specific rules
  • Designed for both human developers and AI agents

Details

The guidelines document covers:

  • Contributing principles — read before edit, minimal focused changes
  • Git workflow — branch off origin/dev, naming conventions, PR targets
  • Code style — Harshil alignment, strict Nextflow syntax, underscore prefix for unused vars
  • Channel operations — join flags, branch/filter over if statements, topic channel migration, scatter-gather pattern
  • Changelog conventions — PR number (not issue number), ascending order, XXX placeholder
  • Configuration — no more if (params.tools...) guards in config files
  • Testing — nf-test patterns, scenario-based structure
  • Documentation — output.md, metro map, citations requirements
  • PR checklist — comprehensive checklist for different change types

Test plan

  • Review document for accuracy against current codebase conventions
  • Verify all code examples are correct and follow stated conventions

🤖 Generated with Claude Code

FriederikeHanssen and others added 3 commits February 20, 2026 11:53
@FriederikeHanssen @claude
Add developer guidelines document
b78158b 
Comprehensive reference covering code style (Harshil alignment, strict
syntax, channel naming), channel operations and gotchas, meta map
handling, module/subworkflow patterns, configuration, testing with
nf-test, documentation requirements, and PR checklist.

Intended for both human developers and AI agents working on sarek.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Move developer guidelines to docs/ and add topic channels guidance
392a94f 
- Move DEVELOPER_GUIDELINES.md to docs/DEVELOPER_GUIDELINES.md
- Add topic channels section (migrating versions collection etc.)
- Remove deprecated if(params.tools) guards from config examples

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Consolidate CLAUDE.md and developer guidelines
629fdd5 
- Add contributing principles, git workflow, and changelog conventions
  to DEVELOPER_GUIDELINES.md so it serves both humans and agents
- Slim CLAUDE.md to a pointer to the guidelines plus agent-only rules

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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nf-core-bot commented Feb 20, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions Bot commented Feb 20, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 720f70c

+| ✅ 224 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-23 16:55:31

FriederikeHanssen and others added 3 commits February 20, 2026 12:16
@FriederikeHanssen @claude
Add variant caller registration checklist to developer guidelines
76d33e7 
Document the 6 locations that must be updated when adding a new
variant caller (schema, dispatcher subworkflows, post_variantcalling
lists, individual subworkflow metadata). Missing any of these causes
silent bugs — especially the small_variantcallers list in
post_variantcalling which silently excludes callers from
normalization/filtering/consensus.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Clarify topic channels and add one-PR-one-feature principle
61c48b3 
- Replace vague topic channel guidance with actionable instruction:
  check if installed/updated modules use topics for versions/multiqc,
  and remove explicit .mix() wiring if so
- Add one-PR-one-feature to contributing principles

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Add pre-commit check, conda setup, and agent behavior rules
eb4f977 
- Add pre-commit requirement to PR checklist in developer guidelines
- Add nf-core conda env and don't-ask-for-confirmation rules to CLAUDE.md

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
heuermh
heuermh reviewed Feb 20, 2026
View reviewed changes
Comment thread docs/DEVELOPER_GUIDELINES.md Outdated
Comment thread docs/DEVELOPER_GUIDELINES.md Outdated
@maxulysse
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maxulysse commented Feb 23, 2026

CHANGELOG?

FriederikeHanssen and others added 4 commits February 23, 2026 17:17
@FriederikeHanssen @claude
Update changelog for developer guidelines PR
f49e8a3 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Add developer guidelines for human and AI contributors
8144247 
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Remove duplicate developer guidelines from root
0da0aba 
The file belongs in docs/DEVELOPER_GUIDELINES.md only.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen @claude
Apply PR review suggestions to developer guidelines
2ed1bc0 
- Remove hardcoded counts from directory tree to avoid staleness
- Remove parentheses rule that conflicts with trailing closure style used elsewhere

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen
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FriederikeHanssen commented Feb 23, 2026

@nf-core-bot fix linting

@FriederikeHanssen FriederikeHanssen merged commit e30dad3 into dev Feb 27, 2026
4 checks passed
@FriederikeHanssen FriederikeHanssen deleted the feat/developer-guidelines branch February 27, 2026 11:43
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@heuermh heuermh heuermh left review comments

@maxulysse maxulysse maxulysse approved these changes

@SPPearce SPPearce Awaiting requested review from SPPearce

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@FriederikeHanssen @nf-core-bot @maxulysse @heuermh