Fix configs

nextflow.config

-profiles {
-  standard {
-    includeConfig 'workflow/config/biohpc.config'
-  }
-  biohpc_local {
-    includeConfig 'workflow/config/biohpc_local.config'
-  }
-  aws_ondemand {
-    includeConfig 'workflow/config/aws_ondemand.config'
-  }
-  aws_spot {
-    includeConfig 'workflow/config/aws_spot.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 {
-  enabled = true
-  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
-}
-
-manifest {
-  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
-  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
-  mainScript = 'main.nf'
-  version = '2.0.0'
-  nextflowVersion = '>=0.31.0'
-}
\ No newline at end of file

workflow/nextflow.config

 profiles {
   standard {
-    includeConfig 'conf/biohpc.config'
+    includeConfig 'configs/biohpc.config'
   }
   biohpc_local {
-    includeConfig 'conf/biohpc_local.config'
+    includeConfig 'configs/biohpc_local.config'
   }
   aws_ondemand {
-    includeConfig 'conf/aws_ondemand.config'
+    includeConfig 'configs/aws_ondemand.config'
   }
   aws_spot {
-    includeConfig 'conf/aws_spot.config'
+    includeConfig 'configs/aws_spot.config'
   }
 }
 
@@ -36,8 +36,8 @@ tower {
 
 manifest {
   homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
-  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
+  description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
   mainScript = 'main.nf'
-  version = '2.0.0'
+  version = '2.0.0-indev'
   nextflowVersion = '>=0.31.0'
-}
\ No newline at end of file
+}