diff --git a/conf/crukmi.config b/conf/crukmi.config index b80343268..7f5c2b74b 100644 --- a/conf/crukmi.config +++ b/conf/crukmi.config @@ -1,54 +1,55 @@ //Profile config names for nf-core/configs params { config_profile_description = 'Cancer Research UK Manchester Institute HPC cluster profile provided by nf-core/configs' - config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)' - config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki' + config_profile_contact = 'Stephen Kitcatt, Simon Pearce (@skitcattCRUKMI, @sppearce)' + config_profile_url = 'http://scicom.picr.man.ac.uk/projects/user-support/wiki' } singularity { - cacheDir = '/lmod/nextflow_software' - enabled = true + cacheDir = '/lmod/nextflow_software' + enabled = true autoMounts = true } process { - beforeScript = 'module load apps/apptainer/1.0.0' - executor = 'slurm' + beforeScript = 'module load apps/apptainer/1.2.0' + executor = 'slurm' + queue = { task.memory <= 240.GB ? 'compute' : 'hmem' } errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'} - maxErrors = '-1' - maxRetries = 3 + maxErrors = '-1' + maxRetries = 3 withLabel:process_single { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } + cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 5.GB * task.attempt, 'memory' ) } } withLabel:process_low { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } + cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 5.GB * task.attempt, 'memory' ) } } withLabel:process_medium { - cpus = { check_max( 4 * task.attempt, 'cpus' ) } + cpus = { check_max( 4 * task.attempt, 'cpus' ) } memory = { check_max( 20.GB * task.attempt, 'memory' ) } } withLabel:process_high { - cpus = { check_max( 48 * task.attempt, 'cpus' ) } - memory = { check_max( 256.GB * task.attempt, 'memory' ) } + cpus = { check_max( 48 * task.attempt, 'cpus' ) } + memory = { check_max( 240.GB * task.attempt, 'memory' ) } } } executor { - name = 'slurm' - queueSize = 1000 + name = 'slurm' + queueSize = 1000 pollInterval = '10 sec' } params { max_memory = 4000.GB - max_cpus = 96 - max_time = 72.h + max_cpus = 96 + max_time = 72.h }