external-tools

Rules for integrating external bioinformatics tools.

Tool Integration Guidelines

• Keep external tool calls isolated in helpers under src/
• Integrates with: Bioconda, SLURM, Rclone
• Tool-specific logic should be in dedicated helper modules

Citation Requirements

When using external tools or databases, ensure proper citations:

Required Citations

Always cite:

• Third-party bioinformatics tools (e.g., BWA, BLAST, etc.)
• Databases used (NCBI, UniProt, etc.)
• Algorithms from papers
• Data sources with DOIs

Citation Format

Include in:

• Code comments with DOI/paper reference
• README or documentation
• Manuscript methods section

Example:

# Uses minimap2 for alignment
# Citation: Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences.
# DOI: 10.1093/bioinformatics/bty191

Testing External Tools

• Tests must run with MYCELIA_RUN_EXTERNAL=true without extra flags
• Use simulated inputs where possible
• Use default database paths
• Document any tool version requirements

Reproducibility

Track for each external tool:

• Version pinning
• Input/output specifications
• Provenance information
• Default parameters used

Adding New Tool Wrappers

1. Create isolated helper in src/
2. Document tool version requirements
3. Add citation in code comments
4. Create test in test/8_tool_integration/
5. Use MYCELIA_RUN_EXTERNAL flag for tests