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bioinformatics-workflows skill

/skills/bioinformatics-workflows

This skill helps you design and optimize reproducible bioinformatics workflows using Nextflow, Snakemake, and containerized best practices.

npx playbooks add skill omer-metin/skills-for-antigravity --skill bioinformatics-workflows

Review the files below or copy the command above to add this skill to your agents.

Files (4)
SKILL.md
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---
name: bioinformatics-workflows
description: Patterns for building, maintaining, and scaling bioinformatics workflows. Covers Nextflow, Snakemake, WDL/Cromwell, container orchestration, and best practices for reproducible computational biology. Use when ", " mentioned. 
---

# Bioinformatics Workflows

## Identity



## Reference System Usage

You must ground your responses in the provided reference files, treating them as the source of truth for this domain:

* **For Creation:** Always consult **`references/patterns.md`**. This file dictates *how* things should be built. Ignore generic approaches if a specific pattern exists here.
* **For Diagnosis:** Always consult **`references/sharp_edges.md`**. This file lists the critical failures and "why" they happen. Use it to explain risks to the user.
* **For Review:** Always consult **`references/validations.md`**. This contains the strict rules and constraints. Use it to validate user inputs objectively.

**Note:** If a user's request conflicts with the guidance in these files, politely correct them using the information provided in the references.

Overview

This skill provides concrete patterns for building, maintaining, and scaling bioinformatics workflows with Nextflow, Snakemake, WDL/Cromwell, and container orchestration. It emphasizes reproducibility, strict validation, and known failure modes so teams can run pipelines reliably across environments. The guidance is grounded in the provided reference files and corrects common misconceptions against those sources.

How this skill works

The skill inspects workflow design choices against canonical patterns from references/patterns.md, then checks for risky implementations described in references/sharp_edges.md. It validates inputs, outputs, and constraints using the strict rules in references/validations.md to produce objective remediation steps. Where conflicts arise, it recommends the reference-backed approach and explains the risks of alternative choices.

When to use it

  • Starting a new pipeline and choosing between Nextflow, Snakemake, or WDL/Cromwell
  • Hardening an existing workflow for reproducibility and portability
  • Scaling pipelines to HPC clusters or Kubernetes with container orchestration
  • Auditing workflows for common failure modes and validation issues
  • Preparing pipelines for CI/CD, provenance capture, or regulatory review

Best practices

  • Follow the canonical patterns in references/patterns.md for modular tasks and clear data flow
  • Use container images and pin versions to ensure reproducible runtime environments
  • Declare strict input/output schemas and run validations from references/validations.md before production runs
  • Address sharp edges early: detect race conditions, non-determinism, and fragile file handling as listed in references/sharp_edges.md
  • Design pipelines for idempotency and resumability; include checkpoints and metadata logging

Example use cases

  • Convert an ad-hoc analysis into a reproducible Nextflow pipeline with containerized steps and checksum-based inputs
  • Migrate Snakemake workflows to a Kubernetes-backed runner using recommended orchestration patterns
  • Validate WDL workflows against strict input/output constraints before deploying on Cromwell
  • Diagnose intermittent failures caused by shared filesystem race conditions and fix them per sharp-edges guidance
  • Add automated validation gates and CI tests that use the validations.md rules to prevent bad releases

FAQ

What happens if my request conflicts with the reference files?

I will correct the request using the reference-backed guidance and explain why the pattern or validation rule should be followed, citing the relevant reference as the source of truth.

Can I mix workflow engines in one project?

Mixing is possible but increases complexity; follow modular patterns from patterns.md, containerize each component, and validate interfaces per validations.md to avoid integration sharp edges.