diff --git a/src/cutadapt.config b/src/cutadapt.config
index 0c2d60a7011f16bab8f5b3650e29651a67cf31fe..247b34aacd07555ebc65bcc9dc19fcf3af7da976 100644
--- a/src/cutadapt.config
+++ b/src/cutadapt.config
@@ -51,3 +51,30 @@ profiles {
   }
 }
 
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $fasta_from_bed {
+        container = "bedtools:2.25.0"
+      }
+    }
+  }
+  sge {
+    process{
+      $fasta_from_bed {
+        beforeScript = "module purge; module load BEDtools/2.25.0"
+        executor = "sge"
+        cpus = 1
+        memory = "5GB"
+        time = "6h"
+        queueSize = 1000
+        pollInterval = '60sec'
+        queue = 'h6-E5-2667v4deb128'
+        penv = 'openmp8'
+      }
+    }
+  }
+}
+