nextflow-implementor

Original：🇺🇸 English

Translated

Nextflow DSL 2 TDD implementation workflow. References nextflow-conventions and agent-conduct.

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Sourcewtsi-hgi/agentskills

Added on2026-04-26

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npx skill4agent add wtsi-hgi/agentskills nextflow-implementor

SKILL.md Content

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Nextflow Implementor Skill

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

TDD Cycle

For each acceptance test, follow every step:

Write a failing nf-test in
```
modules/local/<tool>/tests/main.nf.test
```
.

Run:

nf-test test modules/local/<tool>/tests/main.nf.test

Write minimal process/workflow to pass.
Ensure the process emits
```
versions.yml
```
with tool version(s).
Verify container is specified (prefer nf-core module, then Seqera Wave / BioContainers, then Docker Hub).
Run:
```
nf-core pipelines lint
```
and fix issues.
Re-run nf-test to confirm it passes.

Module-per-Function Rule

Split each tool/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:

bash

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:

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

Specify both docker and singularity container paths.

Workflow

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:

```
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.