checkm2 times out on many samples

[sgavril]

checkm2 seems to time out when running many samples:

ERROR ~ Error executing process > 'NFCORE_PATHOGENSEQ:ILLUMINA:CHECKM2_PREDICT (checkm2)' Caused by: Process exceeded running time limit (4h)

Could possibly change the label for checkm2 from process_single to process_medium?

[xiaoli-dong]

Nice suggestion. I have changed process_single to process_medium for the checkm2 process.

There is another workaround. You can configure the resource available in your local configuration file through the following parameters:

process {

// TODO nf-core: Check the defaults for all processes
cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
memory = { check_max( 6.GB * task.attempt, 'memory' ) }
time   = { check_max( 4.h  * task.attempt, 'time'   ) }

}

You can also configure the resource available for each label through the following parameters in your local configuration file:

process {

withLabel:process_single {
        cpus   = { check_max( 1                  , 'cpus'    ) }
        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
    }
    withLabel:process_low {
        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
    }
    withLabel:process_medium {
        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
    }
    withLabel:process_high {
        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
    }

}