first commit

workflow.wdl

 		call mapping.mapping as mapping {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
-			group=quartet[3],
-			sample=quartet[3],
+			group=quartet[2],
+			sample=quartet[2],
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			ref_dir=ref_dir,
 			sorted_bam=mapping.sorted_bam,
 			sorted_bam_index=mapping.sorted_bam_index,		
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping.sorted_bam,
 			sorted_bam_index=mapping.sorted_bam_index,
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup.Dedup_bam,
 			Dedup_bam_index=Dedup.Dedup_bam_index,
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 			Dedup_bam_index=Dedup.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR.recaled_bam,
 			recaled_bam_index=BQSR.recaled_bam_index,
-			sample=quartet[3],
+			sample=quartet[2],
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config