Add config update (layered)

workflow/conf/aws.config

+aws.client.storageEncryption = 'AES256'
+aws {
+  batch {
+    cliPath = '/home/ec2-user/miniconda/bin/aws'
+  }
+}
+
+process {
+  cpus = 1
+  memory = '10 GB'
+}
\ No newline at end of file

workflow/conf/aws_ondemand.config

+workDir = 's3://gudmap.rbk/work'
+aws {
+  region = 'us-east-2'
+}
+
+process {
+  executor = 'awsbatch'
+  queue = 'highpriority-'
+}
\ No newline at end of file

workflow/conf/aws_spot.config

+workDir = 's3://gudmap.rbk/work'
+aws {
+  region = 'us-east-2'
+}
+
+process {
+  executor = 'awsbatch'
+  queue = 'default-'
+}
\ No newline at end of file

workflow/conf/aws_user.config

+workDir = 's3://'
+aws {
+  region = ''
+}
+
+process {
+  executor = 'awsbatch'
+  queue = ''
+}
\ No newline at end of file

workflow/conf/biohpc.config

 process {
-  executor = 'slurm'
-  queue = 'super'
-  clusterOptions = '--hold'
-
   withLabel: checkDesignFile {
     module = ['python/3.6.1-2-anaconda']
-    executor = 'local'
   }
   withLabel: count211 {
     module = ['cellranger/2.1.1']
-    queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel: count301 {
     module = ['cellranger/3.0.1']
-    queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel: count302 {
     module = ['cellranger/3.0.2']
-    queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel: count310 {
     module = ['cellranger/3.1.0']
-    queue = '128GB,256GB,256GBv1,384GB'
   }
   withLabel: versions {
     module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-    executor = 'local'
   }
   withLabel: multiqc {
     module = ['multiqc/1.7']
-    executor = 'local'
   }
 }
 
@@ -82,25 +71,4 @@ params {
       param = 'SC3Pv3'
     }
   }
-}
-
-trace {
-  enabled = true
-  file = 'pipeline_trace.txt'
-  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
-}
-
-timeline {
-  enabled = true
-  file = 'timeline.html'
-}
-
-report {
-  enabled = true
-  file = 'report.html'
-}
-
-tower {
-  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
-  enabled = true
-}
+}
\ No newline at end of file

workflow/conf/biohpc_cluster.config

+process {
+  executor = 'slurm'
+  queue = 'super'
+  clusterOptions = '--hold'
+
+  withLabel: checkDesignFile {
+    executor = 'local'
+  }
+  withLabel: count211 {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count301 {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count302 {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: count310 {
+    queue = '128GB,256GB,256GBv1,384GB'
+  }
+  withLabel: versions {
+    executor = 'local'
+  }
+  withLabel: multiqc {
+    executor = 'local'
+  }
+}
\ No newline at end of file

workflow/conf/biohpc_local.config

+process {
+  executor = 'local'
+}
\ No newline at end of file