Copy over HPC config

conf/uct_hpc.config

@@ -1,23 +1,41 @@
-//Profile config names for nf-core/configs
+/*
+ * -------------------------------------------------
+ *  HPC cluster config file
+ * -------------------------------------------------
+ * http://www.hpc.uct.ac.za/
+ */
+
 params {
-  config_profile_description = 'University of Cape Town HEX cluster config file provided by nf-core/configs.'
+   config_profile_description = 'University of Cape Town High Performance Cluster config file provided by nf-core/configs.'
-  config_profile_contact = 'Katie Lennard (@kviljoen)'
+   config_profile_contact = 'Katie Lennard (@kviljoen)'
-  config_profile_url = 'http://hpc.uct.ac.za/index.php/hex-3/'
+   config_profile_url = 'http://hpc.uct.ac.za/index.php/hpc-cluster/'
+
+   singularity_cache_dir = "/bb/DB/bio/singularity-containers/"
+   igenomes_base = '/bb/DB/bio/rna-seq/references'
+   max_memory = 384.GB
+   max_cpus = 40
+   max_time = 1000.h
+   hpc_queue = 'ada'
+   hpc_account = '--account cbio'
+   genome = 'GRCh37'
 }
 
 singularity {
    enabled = true
-   cacheDir = "/scratch/DB/bio/singularity-containers"
+   cacheDir = params.singularity_cache_dir
+   autoMounts = true
 }
 
 process {
+   executor = 'slurm'
+   queue = params.hpc_queue
+   // Increasing maxRetries, this will overwrite what we have in base.config
+   maxRetries = 4
+   clusterOptions = params.hpc_account
    stageInMode = 'symlink'
    stageOutMode = 'rsync'
-   queue = 'UCTlong'
-   clusterOptions = { "-M $params.email -m abe -l nodes=1:ppn=1:series600" }
 }
 
-executor{
+executor {
-   executor = 'pbs'
+   queueSize = 15
-   jobName = { "$task.tag" }
 }