Fix nextflow config layering problem

workflow/conf/aws.config

+workDir = 's3://'
 aws.client.storageEncryption = 'AES256'
 aws {
+  region = ''
   batch {
     cliPath = '/home/ec2-user/miniconda/bin/aws'
   }
 }
 
 process {
+  executor = 'awsbatch'
+  queue = 'default-'
   cpus = 1
   memory = '10 GB'
 }
\ No newline at end of file

workflow/conf/aws_ondemand.config

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

workflow/conf/aws_spot.config

-workDir = 's3://'
-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 {
-  withLabel: checkDesignFile {
-    module = ['python/3.6.1-2-anaconda']
-  }
-  withLabel: count211 {
-    module = ['cellranger/2.1.1']
-  }
-  withLabel: count301 {
-    module = ['cellranger/3.0.1']
-  }
-  withLabel: count302 {
-    module = ['cellranger/3.0.2']
-  }
-  withLabel: count310 {
-    module = ['cellranger/3.1.0']
-  }
-  withLabel: versions {
-    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-  }
-  withLabel: multiqc {
-    module = ['multiqc/1.7']
-  }
-}
-
 params {
   // Reference file paths on BioHPC
   genomes {

workflow/conf/biohpc_cluster.config

@@ -4,24 +4,31 @@ process {
   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'
   }
 }
\ No newline at end of file

workflow/conf/biohpc_local.config

 process {
   executor = 'local'
+
+  withLabel: checkDesignFile {
+    module = ['python/3.6.1-2-anaconda']
+  }
+  withLabel: count211 {
+    module = ['cellranger/2.1.1']
+  }
+  withLabel: count301 {
+    module = ['cellranger/3.0.1']
+  }
+  withLabel: count302 {
+    module = ['cellranger/3.0.2']
+  }
+  withLabel: count310 {
+    module = ['cellranger/3.1.0']
+  }
+  withLabel: versions {
+    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+  }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+  }
 }
\ No newline at end of file

workflow/nextflow.config

@@ -11,15 +11,6 @@ profiles {
   aws {
     includeConfig 'conf/aws.config'
   }
-  ondemand {
-    includeConfig 'conf/aws_ondemand.config'
-  }
-  spot {
-    includeConfig 'conf/aws_spot.config'
-  }
-  awsUserDefined {
-    includeConfig 'conf/aws_user.config'
-  }
 }
 
 trace {