diff --git a/conf/utd_ganymede.config b/conf/utd_ganymede.config index 409dc0a..01bb10b 100644 --- a/conf/utd_ganymede.config +++ b/conf/utd_ganymede.config @@ -5,6 +5,11 @@ params { config_profile_url = 'http://docs.oithpc.utdallas.edu/' } +env { + TMPDIR = '/home/$USER/scratch/tmp' + SINGULARITY_CACHEDIR = '/home/$USER/scratch/tmp' +} + singularity { enabled = true envWhitelist='SINGULARITY_BINDPATH' @@ -15,6 +20,28 @@ process { beforeScript = 'module load singularity/3.2.1' executor = 'slurm' 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 {