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enhancementImprovement for existing functionalityImprovement for existing functionality
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SRA is currently mirroring their files on AWS, so it seems like adding an AWS-direct method might be a useful method, particularly for anyone launching workflows in the cloud.
In my own little pipeline, I've set it up like this:
I just give it a samplesheet with an optional SRA column (see schema here) and, if it finds a valid SRA ID for that sample, it will use aws s3 cp
to download the file and feed to fasterq_dump.
This method has been incredibly fast and reliable for me! It would be great to see it in fetchngs.
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enhancementImprovement for existing functionalityImprovement for existing functionality