Merge branch '18-nextflow.configs' into 'develop'

Update nextflow configs to include aws

Closes #18

See merge request !9

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'
+  cpus = 1
+  memory = '1 GB'
+
+  withName:getBag {
+    container = 'bicf/gudmaprbkfilexfer:1.1'
+  }
+  withName:getData {
+    container = 'bicf/gudmaprbkfilexfer:1.1'
+  }
+  withName:trimData {
+    container = 'bicf/trimgalore:1.1'
+    cpus = 15
+  }
+}
\ 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'
+  cpus = 1
+  memory = '1 GB'
+
+  withName:getBag {
+    container = 'bicf/gudmaprbkfilexfer:1.1'
+  }
+  withName:getData {
+    container = 'bicf/gudmaprbkfilexfer:1.1'
+  }
+  withName:trimData {
+    container = 'bicf/trimgalore:1.1'
+    cpus = 15
+  }
+}

workflow/conf/biohpc.config

@@ -3,7 +3,6 @@ process {
   queue = 'super'
   clusterOptions = '--hold'
 
-  // Process specific configuration
   withName:getBag {
     executor = 'local'
     container = 'docker://bicf/gudmaprbkfilexfer:1.1'
@@ -16,45 +15,4 @@ process {
     container = 'docker://bicf/trimgalore:1.1'
     queue = '256GB,256GBv1,384GB'
   }
-}
-
-
-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
-}
-
-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'
-}
-
-manifest {
-  homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
-  description = 'This pipeline was created to analize RNA-sequencing data from GUDMAP/RBK consortiums.'
-  mainScript = 'rna-seq.nf'
-  version = 'v0.0.1_indev'
-  nextflowVersion = '>=19.09.0'
-}
+}
\ No newline at end of file

workflow/nextflow.config

@@ -2,4 +2,39 @@ profiles {
   standard {
     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://git.biohpc.swmed.edu/gudmap_rbk/rna-seq'
+  description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.'
+  mainScript = 'rna-seq.nf'
+  version = 'v0.0.1_indev'
+  nextflowVersion = '>=19.09.0'
+}
\ No newline at end of file