Hi there. I want to run the RNA splice pipeline with a total of 8 cores for all processes and a maximum memory of 48 GB with the options --max_memory '48.GB' --max_cpus 8. But I want to limit the samtools processes to work with 2 cores. I wanted to know if anyone has done something similar and it worked for them. Thanks a lot.

You can do that with a custom config. Put the following in a file (e.g.

samtools.config

):

process {
        withName: 'SAMTOOLS_*' {
                cpus = 2
        }
}

This should apply to any processes with

SAMTOOLS_

in the name, e.g.:

SAMTOOLS_SORT
SAMTOOLS_INDEX
SAMTOOLS_STATS
SAMTOOLS_FLAGSTAT
SAMTOOLS_IDXSTATS

If you want something different, change the

withName:

. You can then use this file with your

nextflow

command using

-c samtools.config

.

Thank you very much it is working!