diff --git a/conf/icr_davros.config b/conf/icr_davros.config new file mode 100644 index 0000000..73e72ed --- /dev/null +++ b/conf/icr_davros.config @@ -0,0 +1,31 @@ +/* + * ------------------------------------------------- + * Nextflow nf-core config file for ICR davros HPC + * ------------------------------------------------- + * Defines LSF process executor and singularity + * settings. + * + */ + +singularity { + enabled = true + runOptions = "--bind /mnt:/mnt --bind /data:/data" +} +executor { + # This is set because of an issue with too many + # singularity containers launching at once, they + # cause an singularity error with exit code 255. + submitRateLimit = "2 sec" +} +process { + executor = "LSF" +} +params { + # LSF cluster set up with memory tied to cores, + # it can't be requested. Locked at 12G per core. + cpus = 10 + max_cpus = 20 + max_memory = 12.GB + max_time = 168.h + igenomes_base = "/mnt/scratch/DDS/SDDS/BIOINFCO/SHARED/genomes/igenomes" +} \ No newline at end of file diff --git a/conf/pipeline/sarek/icr_davros.config b/conf/pipeline/sarek/icr_davros.config new file mode 100644 index 0000000..9c1ea6a --- /dev/null +++ b/conf/pipeline/sarek/icr_davros.config @@ -0,0 +1,8 @@ +process { + errorStrategy = {task.exitStatus in [104,134,137,139,141,143,255] ? 'retry' : 'finish'} + maxRetries = 5 + withName:MapReads { + memory = {check_resource(12.GB)} + time = {check_resource(48.h * task.attempt)} + } +} \ No newline at end of file