update usage

docs/index.md

@@ -111,7 +111,7 @@ picard CreateSequenceDictionary R={ref} O={ref.replace('.fa','.dict')
 
     1) Run it start-to-finish and submit a SBATCH job:
 
-        ```
+        
         #!/bin/bash
         #SBATCH --job-name=searcHPV
         #SBATCH --mail-user=[email protected]
@@ -128,19 +128,19 @@ picard CreateSequenceDictionary R={ref} O={ref.replace('.fa','.dict')
         source ~/anaconda3/etc/profile.d/conda.sh;
         conda activate searcHPV;      
         searcHPV -fastq1 Sample_81279.R1.fastq.gz -fastq2 Sample_81279.R2.fastq.gz -humRef hs37d5.fa -virRef HPV.fa -output /home/scratch/HPV_fusion/Sample_81279 -gz -index;
-        ```
+
 
 
     2) Run it step-by-step:
 
 
-        ```
+        
         searchHPV -alignment -fastq1 Sample_81279.R1.fastq.gz -fastq2 Sample_81279.R2.fastq.gz -humRef hs37d5.fa -virRef HPV.fa -output /home/scratch/HPV_fusion/Sample_81279 -gz -index
         searchHPV -genomeFusion -fastq1 Sample_81279.R1.fastq.gz -fastq2 Sample_81279.R2.fastq.gz -humRef hs37d5.fa -virRef HPV.fa -output /home/scratch/HPV_fusion/Sample_81279 -gz
         searchHPV -assemble -fastq1 Sample_81279.R1.fastq.gz -fastq2 Sample_81279.R2.fastq.gz -humRef hs37d5.fa -virRef HPV.fa -output /home/scratch/HPV_fusion/Sample_81279 -gz
         searchHPV -hpvFusion -fastq1 Sample_81279.R1.fastq.gz -fastq2 Sample_81279.R2.fastq.gz -humRef hs37d5.fa -virRef HPV.fa -output /home/scratch/HPV_fusion/Sample_81279 -gz
 
-        ```
+        
 
     Note: if run it step-by-step, please make sure the output directories for all steps are the same.