Nextflow Implementor
Nextflow DSL 2 TDD implementation workflow. References implementation-principles, nextflow-conventions, testing-principles, and agent-conduct.
Install
$ agentstack add skill-wtsi-hgi-agentskills-nextflow-implementor ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-wtsi-hgi-agentskills-nextflow-implementor) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →About
Nextflow Implementor Skill
Read and follow agent-conduct, implementation-principles, testing-principles, and nextflow-conventions before starting.
Nextflow TDD Steps
- Test location:
modules/local//tests/main.nf.test. - Targeted test:
nf-test test modules/local//tests/main.nf.test - Ensure the process emits
versions.ymlwith tool version(s). - Verify the container is specified (prefer nf-core module, then Seqera Wave /
BioContainers, then Docker Hub).
- Run
nf-core pipelines lintand fix issues.
Module-per-Function Rule
Split each tool/function into its own module under modules/local//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 If a suitable module exists, install it (nf-core modules install ) 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.
After all modules pass, ensure:
nextflow.confighas default params.conf/base.confighas resource labels.conf/modules.confighas publishDir directives.- Profiles work:
docker,singularity,test. - All versions collected into final
versions.yml. docs/usage.mdanddocs/output.mdare written for end-users.
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: wtsi-hgi
- Source: wtsi-hgi/agentskills
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.