add filtering step of reads based on mapping quality >=2

src/RNAseq_sen1D_bowtie2_SE.config

@@ -33,6 +33,9 @@ profiles {
       $mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
+      $quality_filtered_bam {
+        container = "samtools:1.7"
+      }
       $sort_bam {
         container = "samtools:1.7"
       }
@@ -132,6 +135,9 @@ profiles {
       $mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }
+      $quality_filtered_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
       $sort_bam {
         beforeScript = "module purge; module load SAMtools/1.7"
       }