diff --git a/cluster.config b/cluster.config new file mode 100644 index 0000000..6ec18fc --- /dev/null +++ b/cluster.config @@ -0,0 +1,23 @@ +// Configuration settings for NYU Greene HPC Cluster + +params { + max_memory = 3000.GB + max_cpus = 96 + max_time = 7.d +} + +singularity.enabled = true + +process { + executor = 'slurm' + clusterOptions = '--export=NONE' + scratch = true + maxRetries = 3 + errorStrategy = { task.attempt <=3 ? 'retry' : 'finish' } + cache = 'lenient' +} + +executor { + queueSize = 1900 + submitRateLimit = '20 sec' +} diff --git a/launch.sh b/launch.sh index 0d171ea..9f39f18 100644 --- a/launch.sh +++ b/launch.sh @@ -19,6 +19,7 @@ log_dir="/scratch/gencore/GENEFLOW/alpha/logs/${fcid}/pipeline" nextflow_command="nextflow \ -log ${log_dir}/nextflow.log run /home/gencore/SCRIPTS/GENEFLOW/main.nf \ + -c /home/gencore/SCRIPTS/GENEFLOW/cluster.config \ -c /home/gencore/SCRIPTS/GENEFLOW/nextflow.config \ --run_dir_path $run_dir_path \ --trace_file_path ${log_dir}/trace.txt \