This repository contains the example app tutorials that demonstrate how to manipulate and work with the data requested from the St. Jude Cloud Platform. The examples hosted in this repository are meant to serve as a starting point for developing your own application.
For more information on how to request and access datasets and how to write apps and tools to manipulate data in the cloud, refer to the St. Jude Cloud Documentation.
This repository hosts the example tutorial applications located in the Data Guides > Creating a Cloud Application section.
For accessing St. Jude next generation sequencing data and writing cloud applications, you will need a DNAnexus account and dx-toolkit. To explore or manage datasets, refer to our guide Working with Our Data.
dx-adapter-trim- Example application that uses cutadapt to trim sequencing adapters. This app demonstrates providing data to the app via the resources directory. Note this should primarily be used for small, app-specific resources.dx-bam-to-fastq- Example application that extracts FastQ files from aligned BAMs. This app demonstrates returning an array of files as output.dx-bwa-mem- Example application that aligns FastQ files to a reference genome using BWA-MEM. Demonstrates pulling reference files from the common St. Jude Cloud Reference Data project dynamically based on user input for use in the application.dx-cwl-alignment- Example application that aligns FastQ files to a reference genome, sorts the resulting BAM, indexes the BAM, and then produces a flagstat. The pipeline is orchestrated using CWL. The CWL workflow is run in parallel on a single node using multiple cores.dx-fastqc-example-app- Example application used in the Data Guides > Creating a Cloud Application section of the St. Jude Cloud documentation.
This repository is still currently under construction. If you have any additional questions, be sure to contact us!
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