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alesssia / YAMP

YAMP: Yet Another Metagenomic Pipeline
GNU General Public License v3.0
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memory limit #4

Closed SilasK closed 6 years ago

SilasK commented 6 years ago

I'm trying to use YAMP on samples from mouse meta-genome samples. So I downloaded the mouse genome.

During the decontamination step I get a memory error. So I increased the memory limit. Now I'd like to use a higher memory limit for each step, so I don't have to wait too long on the queuing systems.

I found out there are different variables one for $mexmem and another to define the memory fore each process. Do you know hot to use only one variable for both?

alesssia commented 6 years ago

Hello @SilasK,

I just committed a new version that should solve this issue. With this version, you don't need to set up a global number or threads/max memory, but each process will read the correct values directly from the configuration file (nextflow.config), so you can define different values for each process.

Can you please let me know if this is what you need, so I can close the issue?

P.S. mouse metagenome? cool!