first commit

tasks/TNseq.wdl

 task TNseq {
 	File ref_dir
 	File dbsnp_dir
-	Array[String] sample
+	String sample
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String tumor_name
 	String cluster_config
 
 	String fasta
-	Array[File] corealigner_bam
-	Array[File] corealigner_bam_index
+	File corealigner_bam
+	File corealigner_bam_index
 	String dbsnp
 	String disk_size
 	
 			PONcommand=""
 		fi
 		
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${sep=" -i " corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} PONcommand ${sep=" " sample}.TNseq.TN.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} PONcommand ${sample}.TNseq.TN.vcf
 
 	>>>
 
 	}
 
 	output {
-		File TNseq_vcf= "${sep=" " sample}.TNseq.TN.vcf"
-		File TNseq_vcf_index = "${sep=" " sample}.TNseq.TN.vcf.idx"
+		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
+		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
 	}
 
 }

tasks/corealigner.wdl

 	File dbsnp_dir
 	File dbmills_dir
 
-	Array[String] sample
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
 	String docker
 	String cluster_config
 	String fasta
+	String sample
 
 	String dbsnp
 	String db_mills
-	Array[File] tumor_recaled_bam
-	Array[File] tumor_recaled_bam_index
-	Array[File] normal_recaled_bam
-	Array[File] normal_recaled_bam_index
+	File tumor_recaled_bam
+	File tumor_recaled_bam_index
+	File normal_recaled_bam
+	File normal_recaled_bam_index
 	String disk_size
 
 
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 		#${sep=" " tumor_recaled_bam}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${sep=" -i " tumor_recaled_bam} -i ${sep=" -i " normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sep=" " sample}_corealigned.bam				
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${tumor_recaled_bam} -i ${normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sample}_corealigned.bam				
 	>>>
 	
 	runtime {
 	}
 
 	output {
-		File corealigner_bam = "${sep=" " sample}_corealigned.bam"
-		File corealigner_bam_index = "${sep=" " sample}_corealigned.bam.bai"
+		File corealigner_bam = "${sample}_corealigned.bam"
+		File corealigner_bam_index = "${sample}_corealigned.bam.bai"
 	}	
 }