add SAM tools

src/RNAseq_sen1D.config

@@ -89,3 +89,33 @@ profiles {
     }
   }
 }
+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $sort_bam {
+        container = "samtools:1.7"
+      }
+      $index_bam {
+        container = "samtools:1.7"
+      }
+      $split_bam {
+        container = "samtools:1.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $index_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $split_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+    }
+  }
+}