Add agent instructions for repository context

[Copilot]

Configures GitHub Copilot coding agent and other agents with repository-specific context and constraints per best practices.

Changes

• AGENTS.md - 92-line instruction file at repository root covering:
  • Nextflow pipeline architecture (main.nf, fastq_to_ubam.nf, modules/)
  • Critical constraint: legacy/ folder is immutable (historical workflows for paper reproducibility)
  • Testing workflow using nf-test framework
  • Key parameters and configuration structure (conf/references.config, nextflow.config)
  • Development patterns and common operations

Key Context Provided

• EM-seq/E5hmC-seq data processing pipeline structure
• Modular Nextflow DSL2 patterns in modules/ directory
• Testing: nf-test test with snapshot-based validation
• Legacy workflows require NXF_VER=22.10.4 and must remain unchanged

The instructions are placed in AGENTS.md at the repository root so they can be accessed by all agents, not just GitHub Copilot.

Original prompt

---

This section details on the original issue you should resolve

<issue_title>✨ Set up Copilot instructions</issue_title>
<issue_description>Configure instructions for this repository as documented in Best practices for Copilot coding agent in your repository.

</issue_description>

<agent_instructions>ignore the legacy folder, this should be preserved as it is.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes ✨ Set up Copilot instructions #50

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✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.

[bwlang]

@copilot let's use this content but put it in AGENTS.md instead (so other agents can use it)

[Copilot]

@copilot let's use this content but put it in AGENTS.md instead (so other agents can use it)

Done! Moved the content to AGENTS.md in commit 73e373a.

[Copilot]

Pull request overview

This pull request sets up repository-specific guidance for AI coding agents by creating an AGENTS.md file containing comprehensive instructions about the EM-seq pipeline repository structure, development practices, and key constraints.

Changes:

• Added AGENTS.md file with detailed repository documentation and AI agent instructions
• Documented the legacy folder preservation requirement to prevent unintended modifications
• Included project structure, testing guidelines, and development best practices

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💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.