Update configs

workflow/conf/aws_ondemand.config

+workDir = 's3://gudmap.rbk/work'
+aws.client.storageEncryption = 'AES256'
+aws {
+  region = 'us-east-2'
+  batch {
+    cliPath = '/home/ec2-user/miniconda/bin/aws'
+  }
+}
+
+process {
+  executor = 'awsbatch'
+  queue = 'highpriority-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
+}
\ No newline at end of file

workflow/conf/aws_spot.config

+workDir = 's3://gudmap.rbk/work'
+aws.client.storageEncryption = 'AES256'
+aws {
+  region = 'us-east-2'
+  batch {
+    cliPath = '/home/ec2-user/miniconda/bin/aws'
+  }
+}
+
+process {
+  executor = 'awsbatch'
+  queue = 'default-3278a8b0-1fc8-11ea-b1ac-021e2396e2cc'
+}
\ No newline at end of file

workflow/conf/biohpc.config

@@ -30,24 +30,13 @@ process {
   }
 }
 
-
-trace {
+singularity {
   enabled = true
-  file = 'pipeline_trace.txt'
-  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
 }
 
-timeline {
-  enabled = true
-  file = 'timeline.html'
-}
-
-report {
-  enabled = true
-  file = 'report.html'
-}
-
-tower {
-  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
-  enabled = true
-}
+env {
+  http_proxy = 'http://proxy.swmed.edu:3128'
+  https_proxy = 'http://proxy.swmed.edu:3128'
+  all_proxy = 'http://proxy.swmed.edu:3128'
+}
\ No newline at end of file

workflow/conf/biohpc_local.config

+process {
+  executor = 'local'
+}
+
+singularity {
+  enabled = true
+  cacheDir = '/project/shared/bicf_workflow_ref/singularity_images/'
+}
+
+env {
+  http_proxy = 'http://proxy.swmed.edu:3128'
+  https_proxy = 'http://proxy.swmed.edu:3128'
+  all_proxy = 'http://proxy.swmed.edu:3128'
+}
\ No newline at end of file

workflow/nextflow.config

 profiles {
   standard {
+    includeConfig 'conf/biohpc_local.config'
+  }
+  biohpc {
     includeConfig 'conf/biohpc.config'
   }
+  aws_ondemand {
+    includeConfig 'conf/aws_ondemand.config'
+  }
+  aws_spot {
+    includeConfig 'conf/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 {
+  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
+  enabled = true
 }
+
+manifest {
+  homePage = 'https://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 Illumina's bcl2fastq). It takes demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
+  mainScript = 'main.nf'
+  version = 'v1.4.0_indev'
+  nextflowVersion = '>=19.09.0'
+}
\ No newline at end of file