Hello, quick general question on configuration. I am running the pipeline with

-profile ifb_core

and this has a limit on memory of 252, but one of the assemblies in metaspades keeps failing because this is not enough memory. If I modify the max resources on a modified.config, will it overwrite the profile configuration? The alternative will be to deactivate spades and run the pipeline only with megahit or split the coassembly that is running out of memory and do individual assemblies for all samples. I would like to keep the coassembly if possible so, is there a way to overwrite the profile configuration?

Yes 🙂

You likely need to configure the pipeline to your available computational resources to you machine or infrastructure. Please see the following two(!) sections: - https://nf-co.re/docs/usage/getting_started/configuration#tuning-workflow-resources - https://nf-co.re/docs/usage/getting_started/configuration#max-resources of the documentation for more information.

Whatever you supply with

-c

and is shared between both the

-profile

and

-c

config, will be overwritten with the

-c

one taking precendence

Awesome thanks! I wasnt sure if it would!

The general guidance is that MEGAHIT can give you higher quality but shorter contigs, metaSPAdes gives you more complete/contiguous assemblies, but possibly with more errors

I had to remove it because the memory necessary was insane... so I dont have an option any more

You're not alone 😉