Feature request for kneaddata: add option to compress output fastq files

Infrastructure and utilities KneadData
1

I cannot find the option in kneaddata to compress the output fastq files. When running kneaddata in parallel, the output uncompressed fastq files can take up >1T disk space in a day.
Could you add an option to kneaddata to compress the output fastq files?

2

Hi @dwuab ,

Thank you for reaching out to the biobakery lab. We are currently working on getting the option added to Kneaddata and will let you know soon when released.

Regards,
Sagun

1 Like
3

Hi @sagun

Has this update been added to the latest kneadData version? if not then how long is this going to take to add this new feature that can give compressed fastq output from kneadData?

1 Like
4

Hi @sagunmaharjann ,
any news on this option, which is crucial when working with a lot of data?
Your tool is very interesting, but without this option it’s very complicated to use it without exploding the disk space allocated to the project.
Thanks!
Olivier

5

Hi @olivierrue , @saras22 and @dwuab ,

The latest version of biobakery_workflows will compress the fastq files after the kneaddata processing. Please note that kneaddata is part of bioBakery_workflows.

Regards,
Sagun

6

Hi @sagunmaharjann ,
you mean that there will be a compression step for files out of kneaddata in the biobakery_workflows, but not that kneaddata will be able to do it directly, right?
This doesn’t solve the problems of users who want to use kneadata alone, it’s really unfortunate.