Bowtie 2 config

src/RNAseq_sen1D.config

@@ -65,3 +65,27 @@ profiles {
     }
   }
 }
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $index_fasta {
+        container = "bowtie2:2.3.4.1"
+      }
+      $mapping_fastq {
+        container = "bowtie2:2.3.4.1"
+      }
+    }
+  }
+  sge {
+    process{
+      $index_fasta {
+        beforeScript = "module purge; module load Bowtie2/2.3.4.1"
+      }
+      $mapping_fastq {
+        beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
+      }
+    }
+  }
+}