Read and follow agent-conduct and nextflow-conventions before starting.

For each acceptance test, follow every step:

Split each tool/function into its own module under with a corresponding . One process per file, one test file per module.

Before creating a local module, check nf-core:

nf-core modules list remote | grep <tool>

If a suitable module exists, install it () instead of writing a local one. Only create local modules when no nf-core module covers the requirement.

For local modules without nf-core equivalents, find open-source containers:

Specify both docker and singularity container paths.

Implement ONE item at a time: write nf-tests for the spec.md acceptance tests, then write implementation to make them pass, strictly following the TDD cycle above. Consult spec.md for full details.

After all modules pass, ensure: