adding test config

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 = '[email protected]'
+     }
+
+     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
+     }
+   }
+ }
+