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skills/phylo_from_buscos/templates/README.md

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+# Phylogenomics Workflow Templates
+
+This directory contains template scripts for running the phylogenomics pipeline across different computing environments.
+
+## Directory Structure
+
+```
+templates/
+├── slurm/      # SLURM job scheduler templates
+├── pbs/        # PBS/Torque job scheduler templates
+└── local/      # Local machine templates (with GNU parallel support)
+```
+
+## Template Naming Convention
+
+Templates follow a consistent naming pattern: `NN_step_name[_variant].ext`
+
+- `NN`: Step number (e.g., `02` for compleasm, `08a` for partition search)
+- `step_name`: Descriptive name of the pipeline step
+- `_variant`: Optional variant (e.g., `_first`, `_parallel`, `_serial`)
+- `.ext`: File extension (`.job` for schedulers, `.sh` for local scripts)
+
+## Available Templates
+
+### Step 2: Ortholog Identification (compleasm)
+
+**SLURM:**
+- `02_compleasm_first.job` - Process first genome to download lineage database
+- `02_compleasm_parallel.job` - Array job for remaining genomes
+
+**PBS:**
+- `02_compleasm_first.job` - Process first genome to download lineage database
+- `02_compleasm_parallel.job` - Array job for remaining genomes
+
+**Local:**
+- `02_compleasm_first.sh` - Process first genome to download lineage database
+- `02_compleasm_parallel.sh` - GNU parallel for remaining genomes
+
+### Step 8A: Partition Model Selection
+
+**SLURM:**
+- `08a_partition_search.job` - IQ-TREE partition model search with TESTMERGEONLY
+
+**PBS:**
+- `08a_partition_search.job` - IQ-TREE partition model search with TESTMERGEONLY
+
+**Local:**
+- `08a_partition_search.sh` - IQ-TREE partition model search with TESTMERGEONLY
+
+### Step 8C: Individual Gene Trees
+
+**SLURM:**
+- `08c_gene_trees_array.job` - Array job for parallel gene tree estimation
+
+**PBS:**
+- `08c_gene_trees_array.job` - Array job for parallel gene tree estimation
+
+**Local:**
+- `08c_gene_trees_parallel.sh` - GNU parallel for gene tree estimation
+- `08c_gene_trees_serial.sh` - Serial processing (for debugging/limited resources)
+
+## Placeholders
+
+Templates contain placeholders that must be replaced with user-specific values:
+
+| Placeholder | Description | Example |
+|-------------|-------------|---------|
+| `TOTAL_THREADS` | Total CPU cores available | `64` |
+| `THREADS_PER_JOB` | Threads per concurrent job | `16` |
+| `NUM_GENOMES` | Number of genomes in analysis | `20` |
+| `NUM_LOCI` | Number of loci/alignments | `2795` |
+| `LINEAGE` | BUSCO lineage dataset | `insecta_odb10` |
+| `MODEL_SET` | Comma-separated substitution models | `LG,WAG,JTT,Q.pfam` |
+
+## Usage
+
+### For Claude (LLM)
+
+When a user requests scripts for a specific computing environment:
+
+1. **Read the appropriate template** using the Read tool
+2. **Replace placeholders** with user-specified values
+3. **Present the customized script** to the user
+4. **Provide setup instructions** (e.g., how many genomes, how to calculate thread allocation)
+
+Example:
+```python
+# Read template
+template = Read("templates/slurm/02_compleasm_first.job")
+
+# Replace placeholders
+script = template.replace("TOTAL_THREADS", "64")
+script = script.replace("LINEAGE", "insecta_odb10")
+
+# Present to user
+print(script)
+```
+
+### For Users
+
+Templates are not meant to be used directly. Instead:
+
+1. Follow the workflow in `SKILL.md`
+2. Answer Claude's questions about your setup
+3. Claude will fetch the appropriate template and customize it for you
+4. Copy the customized script Claude provides
+
+## Benefits of This Structure
+
+1. **Reduced token usage**: Claude only reads templates when needed
+2. **Easier maintenance**: Update one template file instead of multiple locations in SKILL.md
+3. **Consistency**: All users get the same base template structure
+4. **Clarity**: Separate files are easier to review than inline code
+5. **Extensibility**: Easy to add new templates for additional tools or variants
+
+## Adding New Templates
+
+When adding new templates:
+
+1. **Follow naming convention**: `NN_descriptive_name[_variant].ext`
+2. **Include clear comments**: Explain what the script does
+3. **Use consistent placeholders**: Match existing placeholder names
+4. **Test thoroughly**: Ensure placeholders are complete and correct
+5. **Update this README**: Add the new template to the "Available Templates" section
+6. **Update SKILL.md**: Reference the new template in the appropriate workflow step