Individual skill

bioinformatics-on-healthomics

Guides users through bioinformatics analysis on AWS HealthOmics. Covers analysis type selection (alignment, variant calling, QC, interpretation), workflow generation in Nextflow or WDL, container sourcing from public registries, infrastructure setup (S3, ECR, IAM), workflow registration, parameter preparation, execution, and monitoring. Use when a user wants to run any bioinformatics pipeline on HealthOmics, set up genomics infrastructure on AWS, create a new analysis workflow, or run existing tools like BWA, GATK, DeepVariant, FastQC, or similar on HealthOmics. Triggers include "HealthOmics", "bioinformatics", "genomics pipeline", "Nextflow", "WDL", "BWA", "GATK", "DeepVariant", "FastQC", "variant calling", "alignment", "RNA-seq", "whole genome sequencing", "ECR pull-through", "workflow registration", "run cache"

skills/bioinformatics-on-healthomics/SKILL.md

Source commit 4603541c396cdd845dbae554800a65132d12bb63

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Last checked

Nov 7, 2026

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