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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.
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).
The text was updated successfully, but these errors were encountered:
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 withprefetch
(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.This could be significantly improved by letting
prefetch
grab everything first and while some data is already availablefasterq-dump
could start processing that (similarly to how we do it later for the post-processing steps).The text was updated successfully, but these errors were encountered: