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Decouple fasterq-dump from prefetch to make processing of large datasets faster #95

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misialq opened this issue Feb 25, 2022 · 0 comments
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misialq commented Feb 25, 2022

This enhancement request requires some more evaluation.

In case of large datasets it takes very long for fasterq-dump (blue line in the screenshot below) to process the sequences fetched with prefetch (simply due to the size; red line). As these two actions (prefetch -> fasterq-dump) are currently chained within one function, nothing else can be processed or downloaded before every single sample is done.

Screen Shot 2022-02-25 at 08 43 11

This could be significantly improved by letting prefetch grab everything first and while some data is already available fasterq-dump could start processing that (similarly to how we do it later for the post-processing steps).

@misialq misialq added the enhancement New feature or request label Feb 25, 2022
@misialq misialq added this to the Release follow-up 🔜 milestone Feb 25, 2022
@misialq misialq self-assigned this Jun 15, 2022
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