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Added link to reference setting up ecr
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aolveraNIH committed Nov 26, 2024
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10 changes: 8 additions & 2 deletions Tutorial_4_Nextflow_AWSHealthomics.ipynb
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"id": "f15ea992-faa6-4705-8384-eb5d81f5daff",
"metadata": {},
"source": [
"This short tutorial demonstrates how to run an RNA-Seq workflow using a prokaryotic data set. Steps in the workflow include read trimming, read QC, read mapping, and counting mapped reads per gene to quantitate gene expression. This tutorial uses a popular workflow manager called [Nextflow](https://www.nextflow.io) run via [AWS Healthomics](https://aws.amazon.com/healthomics/). If you completed the other tutorials in this repo, you will see that it is similar to Tutorial 2, but instead of running Snakemake locally, we switch to Nextflow and run it using Healthomics in a serverless manner. "
"This short tutorial demonstrates how to run an RNA-Seq workflow using a prokaryotic data set. Steps in the workflow include read trimming, read QC, read mapping, and counting mapped reads per gene to quantitate gene expression. This tutorial uses a popular workflow manager called [Nextflow](https://www.nextflow.io) run via [AWS Healthomics](https://aws.amazon.com/healthomics/). If you completed the other tutorials in this repo, you will see that it is similar to Tutorial 2, but instead of running Snakemake locally, we switch to Nextflow and run it using Healthomics in a serverless manner. \n",
"\n",
"Before begining this tutorial, if you do not have ECR setup in AWS Sagemaker notebook, please click [here](https://github.com/NIGMS/AWS-HealthOmics-Module-Template/blob/scrnaseq_demo/healthomics_ecr_setup_scrnaseq.ipynb) to set that up."
]
},
{
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]
}
],
"metadata": {},
"metadata": {
"language_info": {
"name": "python"
}
},
"nbformat": 4,
"nbformat_minor": 5
}

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