Running the last process of a pipeline in serial on local executor

[Célie Ds]

Hi there, 

I am new in Nextflow and I am having  an issue that I can't figure out.

Basically, all the processes in my pipeline are executed in a parallel manner, which is fine. However, the last process that need to be executed requires a large amount of free memory (RAM) to work. The issue is that the pipeline crash when running in parallel because there is not enough RAM in the servor to execute it simultaneously on multiple sample.... This way, I was wondering if there was a way to switch from a parallel execution to a serial one on local executor, for this last process. 

Can anybody helps me with this ? 

Thank you, 

Bests,  

Célie

[Sam]

maybe maxForks is what you want

[Theo]

Have you tried to creat a config file that will state for each individual process to run as parallel or as local?

You would need to create an entry like the following:

process {

 withlabel: 'parallel' {

                   executor = "SGE"

                    }

withlabel: 'local' {

                   cpus = 1

                   memory = 120.GB

                    }

                 }

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[Célie Ds]

It worked well with maxForks. 

Thanks you for all of your reply :)