Option of extracting the reads in parser

ClinicalGenomicsGBG / Taxprofiler-Metagenomics

Taxprofiler and Parser on medstore

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Option of extracting the reads in parser #2

Closed SannaAb closed 6 months ago

SannaAb commented 6 months ago

For research samples it might not be important to extract the reads. Specially with diamond as this step is very slow. Allow this to be optional by including an IgnoreReadExtraction flag for each process in diamond, kraken2 and krakenuniq.