correction SAM tools

src/RNAseq_sen1D.config

@@ -94,10 +94,16 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $sort_bam {
+      $sort_bam_forward {
         container = "samtools:1.7"
       }
-      $index_bam {
+      $index_bam_forward {
+        container = "samtools:1.7"
+      }
+      $sort_bam_reverse {
+        container = "samtools:1.7"
+      }
+      $index_bam_reverse {
         container = "samtools:1.7"
       }
       $split_bam {
@@ -107,10 +113,16 @@ profiles {
   }
   sge {
     process{
-      $trimming {
+      $sort_bam_forward {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $index_bam_forward {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $sort_bam_reverse {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $index_bam {
+      $index_bam_reverse {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
       $split_bam {