isabl-run-pipeline

Orchestrate Isabl applications into pipelines for WGS, RNA-Seq, and single-sample analyses.

3|3|Updated Feb 3, 2026

Search Tags:#automation #workflow #analytics #orchestration #bioinformatics #pipeline #isabl

Ready to run

npx skills add https://github.com/juanesarango/isabl-mcp --skill isabl-run-pipeline

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Please help me install this Agent Skill.
Skill: isabl-run-pipeline
Source: https://github.com/juanesarango/isabl-mcp/tree/main/skills/isabl-run-pipeline
Command: npx skills add https://github.com/juanesarango/isabl-mcp --skill isabl-run-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Coordinating and sequencing multiple Isabl applications into end-to-end pipelines to streamline complex analyses.

Core Features & Use Cases

Define pipeline steps (apps and order) to orchestrate diverse analyses.
Stage analyses, submit runs in batch or via API, and monitor progress to completion.
Use cases include WGS tumor-normal pipelines, RNA-Seq workflows, and single-sample analyses with dependent steps.

Quick Start

Define your pipeline steps, stage them, and then submit or monitor the run to completion.

Frequently Asked Questions about isabl-run-pipeline

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I automate a WGS tumor-normal pipeline using Isabl apps?▼

To automate a WGS tumor-normal pipeline, you define the specific Isabl applications as sequential steps, stage the analyses, and submit the runs in batch or via API. The orchestration handles staging, submission, monitoring, and verification to completion.

What is the best way to coordinate multiple bioinformatics apps into a single workflow?▼

Coordinating multiple bioinformatics apps into a single workflow requires orchestrating them into a cohesive pipeline. You specify the apps and their execution order to automate complex sequencing analyses like RNA-Seq or single-sample workflows.

Can I submit and monitor batch bioinformatics pipelines via an API?▼

Yes, you can submit and monitor batch bioinformatics pipelines via API. The system stages your defined pipeline steps and allows batch or API submissions, providing monitoring and verification guardrails until the runs complete.

How do I define steps to sequence Isabl applications for RNA-Seq analyses?▼

You define steps for RNA-Seq analyses by specifying the required Isabl applications and their exact execution order. This configuration allows the pipeline to stage, submit, and monitor the dependent steps automatically.

Does Isabl pipeline orchestration support single-sample analyses with dependent steps?▼

Yes, Isabl pipeline orchestration supports single-sample analyses with dependent steps. You define the sequence of applications, and the system automates the staging, submission, and verification of the entire workflow.

What are the limitations of orchestrating bioinformatics pipelines with dependent steps?▼

Orchestrating bioinformatics pipelines with dependent steps requires accurately defining the app sequence and order beforehand. The system provides monitoring and verification guardrails, but relies on proper step configuration to prevent run failures.