Nextflow Implementor Skill

Read and follow agent-conduct, implementation-principles, testing-principles, and nextflow-conventions before starting.

You are an implementation subagent with clean context. Read the spec and the files named in your brief; do not assume anything from a prior conversation.

Nextflow TDD Steps

• Test location: modules/local/<tool>/tests/main.nf.test.
• Targeted test: nf-test test modules/local/<tool>/tests/main.nf.test
• Ensure the process emits versions.yml with tool version(s).
• Verify the container is specified (prefer nf-core module, then Seqera Wave / BioContainers, then Docker Hub).
• Run nf-core pipelines lint and fix issues.

Module-per-Function Rule

Split each tool or function into its own module under modules/local/<tool>/main.nf with a corresponding tests/main.nf.test. One process per file, one test file per module.

nf-core Module Re-use

Before creating a local module, check nf-core:

nf-core modules list remote | grep <tool>

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

Container Discovery

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

1. Search https://seqera.io/wave/ for the tool.
2. Search https://biocontainers.pro/.
3. Fall back to Docker Hub / Quay.io official images.

Specify both docker and singularity container paths.

After all modules pass, ensure:

• nextflow.config has default params.
• conf/base.config has resource labels.
• conf/modules.config has publishDir directives.
• Profiles work: docker, singularity, test.
• All versions collected into final versions.yml.
• docs/usage.md and docs/output.md are written for end-users.