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Merge pull request #215 from Emiller88/ganymede-update

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Phil Ewels 2021-03-22 19:18:02 +01:00 committed by GitHub
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conf/utd_ganymede.config
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@ -5,6 +5,11 @@ params {
config_profile_url = 'http://docs.oithpc.utdallas.edu/' config_profile_url = 'http://docs.oithpc.utdallas.edu/'
} }
env {
TMPDIR = '/home/$USER/scratch/tmp'
SINGULARITY_CACHEDIR = '/home/$USER/scratch/tmp'
}
singularity { singularity {
enabled = true enabled = true
envWhitelist='SINGULARITY_BINDPATH' envWhitelist='SINGULARITY_BINDPATH'
@ -15,6 +20,28 @@ process {
beforeScript = 'module load singularity/3.2.1' beforeScript = 'module load singularity/3.2.1'
executor = 'slurm' executor = 'slurm'
queue = { task.memory >= 32.GB && task.cpu <= 12 ? 'Kim': task.memory <= 24.GB && task.cpu <= 8 ? 'smallmem' : 'genomics' } queue = { task.memory >= 32.GB && task.cpu <= 12 ? 'Kim': task.memory <= 24.GB && task.cpu <= 8 ? 'smallmem' : 'genomics' }
withName:TRIMGALORE {
memory = 31.GB
}
withLabel:process_low {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 12.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withLabel:process_medium {
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 31.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( 120.GB * task.attempt, 'memory' ) }
time = { check_max( 16.h * task.attempt, 'time' ) }
}
} }
params { params {