Fix bug: workflow input

tasks/processSomatic.wdl

 	String sample
 	File varscan_snp
 	File varscan_indel
-    
-	File ref_dir
-    String fasta
+	
     String docker
     String cluster_config
     String disk_size

workflow.wdl

         input:
         sample=sample_id,
         varscan_snp=somatic.varscan_snp,
-        varscan_indel=somatic.varscan_indel,
-        ref_dir=ref_dir,
-        fasta=fasta,        
+        varscan_indel=somatic.varscan_indel,     
         docker=varscan_docker,	
         disk_size=disk_size,
         cluster_config=cluster_config
         varscan_snp_loh_hc=processSomatic.varscan_snp_loh_hc,
         varscan_indel_somatic_hc=processSomatic.varscan_indel_somatic_hc,
         varscan_indel_loh_hc=processSomatic.varscan_indel_loh_hc,
-        varscan_indel=somatic.varscan_indel,
-        ref_dir=ref_dir,
-        fasta=fasta,        
+        varscan_indel=somatic.varscan_indel,   
         docker=varscan_docker,	
         disk_size=disk_size,
         cluster_config=cluster_config
     }
-    
+
     call annovar.annovar as snp_somatic_annovar {
         input: 
         sample=sample_id,