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Create example of running Nextflow workflow on TES #589

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MattMcL4475 opened this issue Feb 3, 2024 · 0 comments
Open

Create example of running Nextflow workflow on TES #589

MattMcL4475 opened this issue Feb 3, 2024 · 0 comments
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enhancement New feature or request

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@MattMcL4475
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  1. Create a TES task, that uses an official Nextflow docker image, OR, uses Ubuntu and downloads and installs and configures Nextflow at startup. Nextflow shall be configured to use TES as a backend, and the TES API shall be set as https://tes/v1. (TODO: need to ensure the TES pod in AKS has a host record in the local DNS, so that the Batch node can connect to it) That same TES task shall also specify the genomics inputs from the 1000 genomes storage account (Azure Open Datasets Genomics Data Lake), and also specify for Nextflow to run the RNA Seq pipeline:
    https://www.nextflow.io/example4.html
  2. The original TES task shall run with preemptible false, on a small VM, ideally 1 core or less, to save on cost.
  3. The command script should continually query Nextflow (in the idiomatic Nextflow way) to check if the workflow is done. Once it is done, the command script shall exit, which will complete the TES task.
@MattMcL4475 MattMcL4475 added Performance Enable users can run task as cheap and as fast as possible enhancement New feature or request and removed Performance Enable users can run task as cheap and as fast as possible labels Feb 3, 2024
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