Run Multiple Files in one time

[Faisal]

Dear All,

Thank you for this script and providing the support for the user.

I tried to make the first run but I noticed it does not support providing a folder as input for multiple file of fastq.gz. It required to make it one by one. I have 117 samples. Is there any way to automate this process?

Also, I am looking to way to count the reads number before doing any filteration for human reads and after remove these reads and after trimming. I hope this script can do this as this will help to nderstand where is the lost happen specially for trimming step.

Regards,

Faisal

[Lauren McIver]

Hello Faisal, Yes, the biobakery workflows wmgx workflow includes kneaddata. You can use this to run kneaddata on a folder of files. One of the output files from the workflow is a table of read counts. If you just want to run kneaddata (and not the other steps like metaphlan2/humann2/strainphlan) there are bypass options you can add when you run your workflow. Here is a link to the documentation. Please let me know if you have any other questions. http://huttenhower.sph.harvard.edu/biobakery_workflows 

Thank you,

Lauren

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