sample name

tasks/BQSR.wdl

     File ref_dir
     File dbsnp_dir
     File dbmills_dir
-	String sample
 	String SENTIEON_INSTALL_DIR
 	String fasta
 	String dbsnp
 	String db_mills
 	File realigned_bam
 	File realigned_bam_index
+	String sample = basename(realigned_bam,".sorted.deduped.realigned.bam")
 	String docker
 	String cluster_config
 	String disk_size

tasks/Dedup.wdl

 task Dedup {
 
 	String SENTIEON_INSTALL_DIR
-	String sample
-
 	File sorted_bam
 	File sorted_bam_index
+	String sample = basename(sorted_bam,".sorted.bam")
 	String docker
 	String cluster_config
 	String disk_size

tasks/Haplotyper.wdl

 	String fasta
 	File recaled_bam
 	File recaled_bam_index
-	String sample
+	String sample = basename(recaled_bam,".sorted.deduped.realigned.recaled.bam")
 	String docker
 	String cluster_config
 	String disk_size

tasks/Realigner.wdl

     File dbmills_dir
 
 	String SENTIEON_INSTALL_DIR
-	String sample
 	String fasta
 
 	File Dedup_bam
 	File Dedup_bam_index
+	String sample = basename(Dedup_bam,".sorted.deduped.bam")
 	String db_mills
 	String docker	
 	String cluster_config

tasks/deduped_Metrics.wdl

 
     File ref_dir
 	String SENTIEON_INSTALL_DIR
-	String sample
 	String fasta
 	File Dedup_bam
 	File Dedup_bam_index
+	String sample = basename(Dedup_bam,".sorted.deduped.bam")
 	String docker
 	String cluster_config
 	String disk_size

tasks/mapping.wdl

 
 	String SENTIEON_INSTALL_DIR
 	String SENTIEON_LICENSE
-	String group
-	String sample
+	String group = basename(fastq_1,"_R1.fastq.gz")
+	String sample = basename(fastq_1,"_R1.fastq.gz")
 	String pl
 	String docker
 	String cluster_config

tasks/sentieon.wdl

 	File aln_metrics
 	File is_metrics
 
-	String sample
+	String sample = basename(quality_yield,"_deduped_QualityYield.txt")
 	String docker
 	String cluster_config
 	String disk_size

workflow.wdl

 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL5",
-			sample="LCL5",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_D5.sorted_bam,
 			sorted_bam_index=mapping_D5.sorted_bam_index,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D5.Dedup_bam,
 			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_D5.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_D5.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_D5.deduped_is_metrics,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_D5.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_D5.recaled_bam,
 			recaled_bam_index=BQSR_D5.recaled_bam_index,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL6",
-			sample="LCL6",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_D6.sorted_bam,
 			sorted_bam_index=mapping_D6.sorted_bam_index,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_D6.Dedup_bam,
 			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_D6.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_D6.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_D6.deduped_is_metrics,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_D6.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_D6.recaled_bam,
 			recaled_bam_index=BQSR_D6.recaled_bam_index,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL7",
-			sample="LCL7",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_F7.sorted_bam,
 			sorted_bam_index=mapping_F7.sorted_bam_index,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_F7.Dedup_bam,
 			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_F7.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_F7.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_F7.deduped_is_metrics,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_F7.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_F7.recaled_bam,
 			recaled_bam_index=BQSR_F7.recaled_bam_index,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL8",
-			sample="LCL8",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			sorted_bam=mapping_M8.sorted_bam,
 			sorted_bam_index=mapping_M8.sorted_bam_index,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			Dedup_bam=Dedup_M8.Dedup_bam,
 			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			wgs_metrics_algo=deduped_Metrics_M8.deduped_wgsmetrics,
 			aln_metrics=deduped_Metrics_M8.dedeuped_aln_metrics,
 			is_metrics=deduped_Metrics_M8.deduped_is_metrics,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size		
 			Dedup_bam_index=Dedup_M8.Dedup_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
 			ref_dir=ref_dir,
 			recaled_bam=BQSR_M8.recaled_bam,
 			recaled_bam_index=BQSR_M8.recaled_bam_index,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config