diff --git a/conf/cdc.config b/conf/cdc.config new file mode 100755 index 0000000..7744f73 --- /dev/null +++ b/conf/cdc.config @@ -0,0 +1,81 @@ +env { + TMPDIR = "$HOME/tmp" +} + +singularity { + enabled = true + autoMounts = true + cacheDir = "$HOME/singularityIMG2" +} + +profiles { + rosalind { + executor { + name = 'sge' + queueSize = 12 + pollInterval = '10sec' + submitRateLimit = '2sec' + } + process { + // Executor information + executor = 'sge' + //jobName = { "$task.name - $task.hash" } + penv = 'smp' + queue = { task.time <= 4.h ? 'short.q' : task.time > 7.day ? 'long.q' : 'all.q' } + + // Disable docker by default + docker.enabled = false + + // Default resources - expected to be overwritten + memory = '90.GB' + cpus = 16 + time = '96.h' + + // Set h_vmem option for qsub submissions. +20 memory to h_vmem prevents memory allocation errors. + clusterOptions = { "-l h_vmem=${(check_max((task.memory.toGiga())+20), 'memory').toString().replaceAll(/[\sB]/,'')}G" } + + // Error handling - increases resources on each retry. Try to ignore errors and continue if not in errors listed. + errorStrategy = { task.exitStatus in [143,137,104,134,139,140,71,255] ? 'retry' : 'ignore' } + maxRetries = 3 + maxErrors = '-1' + } + } + sge { + process { + executor = 'sge' + penv = 'smp' + queue = 'all.q' + } + + executor { + queueSize = 96 + } + } + sgecannon { + process { + //beforeScript = 'source /etc/profile; module load singularity/3.5.3' + beforeScript = 'source /scicomp/groups-pure/Projects/scbs_mpob/miniconda3.9/bin/activate /scicomp/groups-pure/Projects/scbs_mpob/miniconda3.9/envs/nextflow' + executor = 'sge' + penv = 'smp' + queue = 'all.q,covid.q' + //queue = 'covid.q@node61.hpc.biotech.cdc.gov' + } + + executor { + queueSize = 32 + } + } + sgeaspen { + process { + beforeScript = 'source /scicomp/groups-pure/Projects/scbs_mpob/miniconda3.9/bin/activate /scicomp/groups-pure/Projects/scbs_mpob/miniconda3.9/envs/nextflow' + executor = 'sge' + penv = 'smp' + queue = 'short.q,all.q' + } + + executor { + queueSize = 64 + } + } + } +