Generate sequence structure mapping files for any organism

.claude/README.md

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+# Claude Code Configuration
+
+This directory contains configuration and hooks for Claude Code development sessions.
+
+## Session Start Hook
+
+The `hooks/SessionStart` script runs automatically when you start a Claude Code session. It:
+
+- Verifies conda/mamba is available
+- Checks if the `aatrnaseqpipe` environment exists (creates it if not)
+- Activates the environment
+- Validates Snakemake installation
+- Validates configuration files
+- Sets up pre-commit hooks
+- Runs a quick Snakemake syntax check
+
+This ensures your development environment is properly configured before starting work.
+
+## Manual Testing
+
+You can run the session start hook manually:
+
+```bash
+bash .claude/hooks/SessionStart
+```
+
+## Development Workflow
+
+1. **Before making changes**: Run `bash .tests/run_local_tests.sh` to verify everything works
+2. **During development**: Use `snakemake -n --configfile=config/config-test.yml` for syntax checks
+3. **Before committing**: Pre-commit hooks will automatically run linting and formatting
+4. **After committing**: GitHub Actions will run full CI/CD checks
+
+## Learn More
+
+- Project documentation: `CLAUDE.md`
+- Local test script: `.tests/run_local_tests.sh`
+- CI/CD workflows: `.github/workflows/`
+- Pre-commit config: `.pre-commit-config.yaml`

.claude/SETUP.md

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+# Complete Test and Build Check Setup
+
+This document describes the comprehensive test and build infrastructure for the aa-tRNA-seq-pipeline.
+
+## ✅ What's Installed
+
+### 1. GitHub Actions CI/CD
+
+**Location**: `.github/workflows/`
+
+#### CI Pipeline (`ci.yml`)
+Runs on: push to main/master/develop/claude/**, pull requests, manual trigger
+
+- **Syntax Check Job**
+  - Sets up conda environment with Snakemake
+  - Validates Snakemake syntax with dry-run
+
+- **Pipeline Integration Test Job**
+  - Downloads test data
+  - Sets up dorado and modkit tools
+  - Runs merge_pods rule (non-GPU test)
+  - Validates output directory creation
+
+- **Configuration Validation Job**
+  - Validates YAML syntax in all config files
+  - Checks samples.tsv files exist and have content
+  - Verifies required directory structure
+
+#### Lint Pipeline (`lint.yml`)
+Runs on: push to main/master/develop/claude/**, pull requests, manual trigger
+
+- **Snakemake Linting**: snakefmt format checking
+- **Python Linting**: black and flake8 on workflow/scripts/
+- **Markdown Linting**: markdownlint on all .md files
+- **YAML Linting**: yamllint on config/ and .github/
+
+### 2. Pre-commit Hooks
+
+**Location**: `.pre-commit-config.yaml`
+
+Automatically runs before each commit:
+- Trailing whitespace removal
+- End-of-file fixing
+- YAML syntax validation
+- Large file detection (>1MB warning)
+- Merge conflict detection
+- Line ending normalization
+- Black formatting for Python scripts
+- Flake8 linting for Python scripts
+- Snakefmt formatting for Snakemake files
+
+**Installation**:
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+### 3. Local Test Script
+
+**Location**: `.tests/run_local_tests.sh`
+
+Runs the same checks as CI locally:
+1. Verifies Snakemake installation
+2. Validates configuration files (YAML syntax)
+3. Checks sample files exist
+4. Runs Snakemake dry-run (syntax check)
+5. Verifies required directory structure
+
+**Usage**:
+```bash
+# Requires active conda environment
+mamba activate aatrnaseqpipe
+bash .tests/run_local_tests.sh
+```
+
+### 4. Claude Code Session Hooks
+
+**Location**: `.claude/hooks/SessionStart`
+
+Automatically runs when starting a Claude Code session:
+- Verifies conda/mamba availability
+- Creates aatrnaseqpipe environment if missing
+- Activates the environment
+- Validates Snakemake installation
+- Checks config file syntax
+- Installs pre-commit hooks if not present
+- Runs quick Snakemake syntax check
+- Displays helpful development commands
+
+## 📋 Development Workflow
+
+### Starting a New Session
+
+When you start working with Claude Code, the SessionStart hook automatically:
+1. Sets up your environment
+2. Validates configurations
+3. Shows available commands
+
+### Before Making Changes
+
+```bash
+# Run full local test suite
+bash .tests/run_local_tests.sh
+
+# Or just syntax check
+snakemake -n --configfile=config/config-test.yml
+```
+
+### During Development
+
+```bash
+# Test specific rule
+snakemake <rule_name> -n --configfile=config/config-test.yml
+
+# Run linting manually
+pre-commit run --all-files
+
+# Format Snakemake files
+snakefmt workflow/
+
+# Format Python scripts
+black workflow/scripts/
+```
+
+### Before Committing
+
+Pre-commit hooks run automatically. If they fail:
+```bash
+# Fix issues and re-stage
+git add <fixed-files>
+
+# Or skip hooks (not recommended)
+git commit --no-verify
+```
+
+### After Pushing
+
+GitHub Actions automatically runs:
+- All syntax checks
+- Integration tests
+- All linters
+- Configuration validation
+
+Check status at: `https://github.com/<owner>/<repo>/actions`
+
+## 🧪 Testing Levels
+
+### Level 1: Quick Validation (< 30 seconds)
+```bash
+# Config and syntax only
+python3 -c "import yaml; yaml.safe_load(open('config/config-test.yml'))"
+snakemake -n --configfile=config/config-test.yml
+```
+
+### Level 2: Local Tests (~ 2 minutes)
+```bash
+# Full local test suite
+bash .tests/run_local_tests.sh
+```
+
+### Level 3: Integration Test (~ 10-15 minutes)
+```bash
+# Download test data (first time only)
+bash .tests/dl_test_data.sh
+
+# Setup tools (first time only)
+snakemake setup_dorado dorado_model setup_modkit --cores 1 --configfile=config/config-test.yml
+
+# Run non-GPU pipeline rules
+snakemake merge_pods --cores 2 --configfile=config/config-test.yml
+```
+
+### Level 4: Full Pipeline (requires GPU)
+```bash
+# Run complete pipeline with test data
+snakemake --cores 12 --configfile=config/config-test.yml
+
+# Or submit to LSF cluster
+bsub < run-test.sh
+```
+
+## 🔍 Continuous Integration Details
+
+### What Gets Tested on Every Push
+
+1. **Snakemake syntax**: Dry-run validation
+2. **Config files**: YAML syntax validation
+3. **Sample files**: Existence and content checks
+4. **Directory structure**: Required directories present
+5. **Code formatting**: Black, flake8, snakefmt
+6. **Documentation**: Markdown linting
+
+### What Gets Tested on Pull Requests
+
+All of the above, plus:
+- Integration test with test data
+- Tool setup (dorado, modkit)
+- Pipeline execution (non-GPU rules)
+
+### What's NOT Tested in CI
+
+Due to GitHub Actions limitations:
+- GPU-intensive rules (rebasecall, classify_charging)
+- Full end-to-end pipeline
+- LSF cluster execution
+
+These should be tested locally or on your cluster before merging.
+
+## 🛠️ Maintenance
+
+### Updating Dependencies
+
+```bash
+# Update conda environment
+mamba env update -n aatrnaseqpipe -f workflow/envs/aatrnaseqpipe-env.yml
+
+# Update pre-commit hooks
+pre-commit autoupdate
+```
+
+### Adding New Tests
+
+1. **Local tests**: Edit `.tests/run_local_tests.sh`
+2. **CI tests**: Edit `.github/workflows/ci.yml`
+3. **Linting**: Edit `.pre-commit-config.yaml` and `.github/workflows/lint.yml`
+
+### Troubleshooting
+
+**Pre-commit hooks failing?**
+```bash
+# Run manually to see detailed errors
+pre-commit run --all-files
+
+# Update hooks to latest versions
+pre-commit autoupdate
+```
+
+**CI failing but local tests pass?**
+- Check GitHub Actions logs for specific errors
+- Ensure all files are committed
+- Verify config files are valid YAML
+
+**SessionStart hook not running?**
+- Check if Claude Code session hooks are enabled
+- Run manually: `bash .claude/hooks/SessionStart`
+- Ensure file is executable: `chmod +x .claude/hooks/SessionStart`
+
+## 📚 Additional Resources
+
+- **Project Overview**: `CLAUDE.md`
+- **CI Workflows**: `.github/workflows/`
+- **Pre-commit Config**: `.pre-commit-config.yaml`
+- **Test Scripts**: `.tests/`
+- **Snakemake Docs**: https://snakemake.readthedocs.io/