diff --git a/nextflow.config b/nextflow.config
deleted file mode 100644
index f1a8650838d6edf16f407869d9645ed11e75c264..0000000000000000000000000000000000000000
--- a/nextflow.config
+++ /dev/null
@@ -1,52 +0,0 @@
-profiles {
-  biohpc {
-    includeConfig 'conf/biohpc.config'
-  }
-  local {
-    includeConfig 'conf/biohpc_local.config'
-  }
-  cluster {
-    includeConfig 'conf/biohpc_cluster.config'
-  }
-  aws {
-    includeConfig 'conf/aws.config'
-  }
-  ondemand {
-    includeConfig 'conf/aws_ondemand.config'
-  }
-  spot {
-    includeConfig 'conf/aws_spot.config'
-  }
-  awsUserDefined {
-    includeConfig 'conf/aws_user.config'
-  }
-}
-
-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
-}
-
-manifest {
-  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
-  description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
-  mainScript = 'main.nf'
-  version = 'v1.2.1_indev'
-  nextflowVersion = '>=0.31.0'
-}
\ No newline at end of file
diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 30e47ea1aea37ed6550cc2944d69d26e69887489..f1a8650838d6edf16f407869d9645ed11e75c264 100644
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,5 +1,52 @@
 profiles {
-  standard {
+  biohpc {
     includeConfig 'conf/biohpc.config'
   }
+  local {
+    includeConfig 'conf/biohpc_local.config'
+  }
+  cluster {
+    includeConfig 'conf/biohpc_cluster.config'
+  }
+  aws {
+    includeConfig 'conf/aws.config'
+  }
+  ondemand {
+    includeConfig 'conf/aws_ondemand.config'
+  }
+  spot {
+    includeConfig 'conf/aws_spot.config'
+  }
+  awsUserDefined {
+    includeConfig 'conf/aws_user.config'
+  }
+}
+
+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
 }
+
+manifest {
+  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count'
+  description = 'This pipeline is a wrapper for the cellranger count tool from 10x Genomics. It takes fastq files from 10x Genomics Single Cell Gene Expression libraries, performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate gene-barcode matrices, determine clusters, and perform gene expression analysis.'
+  mainScript = 'main.nf'
+  version = 'v1.2.1_indev'
+  nextflowVersion = '>=0.31.0'
+}
\ No newline at end of file