Skills latchbio-integration

📦

latchbio-integration

Name: latchbio-integration
Author: davila7

Content revision r2 Safe 📁 Filesystem access🔑 Env variables⚡ Contains scripts⚙️ External commands🌐 Network access

Build and Deploy Latch Bioinformatics Workflows

Bioinformatics teams need reproducible workflows without managing complex infrastructure. This skill guides Latch workflow creation, cloud data handling, resource configuration, and deployment.

Supports: Claude Codex Code(CC)

📊 76 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "latchbio-integration" from https://skillstore.io/skills/davila7-latchbio-integration.md and its manifest at https://skillstore.io/api/skills/davila7-latchbio-integration/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/davila7-latchbio-integration.md Signed manifest GET /api/skills/davila7-latchbio-integration/manifest Signed lockfile GET /api/skills/davila7-latchbio-integration/lockfile

Test it

Using "latchbio-integration". Plan a small RNA-seq workflow for paired FASTQ files.

Expected outcome:

Inputs: paired FASTQ files, genome reference, and an output directory.
Tasks: quality control, alignment, and quantification with typed outputs.
Resources: start small for quality control and quantification, then use a larger alignment task.
Validation: test locally with Docker before registering the workflow.

Using "latchbio-integration". Recommend resources for an AlphaFold task.

Expected outcome:

Use a GPU task because AlphaFold benefits from supported acceleration.
Estimate memory and temporary storage from sequence length and database requirements.
Set a conservative timeout, then revise it using observed execution metrics.

Using "latchbio-integration". Troubleshoot a failed Latch registration.

Expected outcome:

Confirm Docker is running and Latch authentication is valid.
Verify dependencies and workflow type annotations.
Repeat registration with verbose logging and review the first reported error.

Security Audit

Safe

v9 • 7/23/2026 Open versioned report

All 30 static findings are false positives caused by documentation examples, Markdown formatting, standard platform APIs, and official resource links. No prompt injection, credential exfiltration, unsafe command construction, or malicious intent was found.

Files scanned

1,949

Lines analyzed

Review items

False positives ignored

Risk Factors

📁 Filesystem access (2)

references/data-management.md:64 references/resource-configuration.md:276

🔑 Env variables (1)

references/data-management.md:380

⚡ Contains scripts (1)

references/verified-workflows.md:13-20

⚙️ External commands (21)

🌐 Network access (4)

SKILL.md:335 SKILL.md:336 SKILL.md:338 SKILL.md:339

No confirmed security findings were detected by the latest completed static and semantic audit. This does not prove the skill has no side effects.

Audited by: codex View Audit History →

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Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). latchbio-integration security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-latchbio-integration/audits/9

BibTeX citation

@techreport{davila7-davila7-latchbio-integration-2026,
  author = {davila7},
  title = {latchbio-integration security audit report (audit version 9)},
  institution = {Skillstore},
  year = {2026},
  number = {9},
  url = {https://skillstore.io/skills/davila7-latchbio-integration/audits/9},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "latchbio-integration security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-latchbio-integration/audits/9"
identifiers:
  - type: other
    value: "skillstore:davila7-latchbio-integration:audit:9"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended Current

davila7-latchbio-integration

Skillstore Score 76

Evidence Confidence High

Skillstore usage 6

Updated

2026-08-21

K-Dense-AI

k-dense-ai-latchbio-integration

Skillstore Score 38

Evidence Confidence Medium

Skillstore usage 10

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Create a Genomics Pipeline

Design a typed Latch workflow for quality control, alignment, quantification, and cloud outputs.

Move Existing Workflows

Plan the integration of an existing Nextflow or Snakemake pipeline with Latch deployment and storage.

Right-Size Cloud Tasks

Choose practical CPU, memory, GPU, storage, and timeout settings for research workloads.

Try These Prompts

Explain the Latch Structure

Explain how workflows, tasks, LatchFile, and LatchDir fit together for a beginner building a simple sequencing pipeline.

Design a Workflow

Design a Latch RNA-seq workflow with quality control, alignment, and quantification. List inputs, outputs, task boundaries, and recommended decorators.

Configure Resources

Review these workload requirements: [requirements]. Recommend Latch CPU, memory, GPU, storage, timeout, and parallelization settings with brief reasons.

Plan a Pipeline Migration

Create a migration plan for this [Nextflow or Snakemake] pipeline: [pipeline details]. Cover dependencies, data paths, resources, registration, testing, and rollback.

Best Practices

Use explicit types, clear docstrings, and modular task boundaries for reproducible workflows.
Test locally with Docker and review generated artifacts before registration.
Start with standard resources, monitor real usage, and increase capacity only when evidence supports it.

Avoid

Do not place credentials in workflow code, prompts, logs, or committed configuration.
Do not over-allocate GPU, memory, or storage without workload measurements.
Do not register untested pipelines or overwrite production workflow versions without review.

Frequently Asked Questions

Does this skill run workflows automatically?

No. It provides implementation guidance. Running or registering a workflow requires tools, credentials, and user-approved command execution.

Which pipeline formats are covered?

The references cover native Python workflows plus integration approaches for Nextflow and Snakemake.

Can it help choose compute resources?

Yes. It explains standard and custom task configurations for CPU, memory, GPU, storage, and timeout requirements.

How does it handle workflow data?

It documents LatchFile, LatchDir, cloud paths, Registry records, tables, links, transactions, and launch plans.

Are verified workflows included?

It documents how to import and combine selected Latch verified workflows. Availability and interfaces should be checked against current Latch documentation.

What must be installed before deployment?

Deployment generally requires Python, the Latch SDK, Docker, and valid Latch account credentials.