gh-brunoasm-my-claude-skills-bioinfo-skills/skills/phylo_from_buscos/templates/README.md

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:

# 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