sample name

tasks/BQSR.wdl

@@ -3,13 +3,13 @@ task BQSR {
     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

@@ -1,10 +1,9 @@
 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

@@ -5,7 +5,7 @@ task Haplotyper {
 	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

@@ -4,11 +4,11 @@ task Realigner {
     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

@@ -2,10 +2,10 @@ task deduped_Metrics {
 
     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

@@ -7,8 +7,8 @@ task mapping {
 
 	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

@@ -4,7 +4,7 @@ task sentieon {
 	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

@@ -73,8 +73,6 @@ workflow {{ project_name }} {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL5",
-			sample="LCL5",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
@@ -110,7 +108,6 @@ workflow {{ project_name }} {
 			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
@@ -132,7 +129,6 @@ workflow {{ project_name }} {
 			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
@@ -144,7 +140,6 @@ workflow {{ project_name }} {
 			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		
@@ -159,7 +154,6 @@ workflow {{ project_name }} {
 			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
@@ -176,7 +170,6 @@ workflow {{ project_name }} {
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL5",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
@@ -189,7 +182,6 @@ workflow {{ project_name }} {
 			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
@@ -218,8 +210,6 @@ workflow {{ project_name }} {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL6",
-			sample="LCL6",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
@@ -255,7 +245,6 @@ workflow {{ project_name }} {
 			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
@@ -277,7 +266,6 @@ workflow {{ project_name }} {
 			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
@@ -289,7 +277,6 @@ workflow {{ project_name }} {
 			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		
@@ -304,7 +291,6 @@ workflow {{ project_name }} {
 			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
@@ -321,7 +307,6 @@ workflow {{ project_name }} {
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL6",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
@@ -334,7 +319,6 @@ workflow {{ project_name }} {
 			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
@@ -363,8 +347,6 @@ workflow {{ project_name }} {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL7",
-			sample="LCL7",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
@@ -400,7 +382,6 @@ workflow {{ project_name }} {
 			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
@@ -422,7 +403,6 @@ workflow {{ project_name }} {
 			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
@@ -434,7 +414,6 @@ workflow {{ project_name }} {
 			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		
@@ -449,7 +428,6 @@ workflow {{ project_name }} {
 			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
@@ -466,7 +444,6 @@ workflow {{ project_name }} {
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL7",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
@@ -479,7 +456,6 @@ workflow {{ project_name }} {
 			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
@@ -508,8 +484,6 @@ workflow {{ project_name }} {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			group="LCL8",
-			sample="LCL8",
 			pl="ILLUMINAL",
 			fasta=fasta,
 			ref_dir=ref_dir,
@@ -545,7 +519,6 @@ workflow {{ project_name }} {
 			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
@@ -567,7 +540,6 @@ workflow {{ project_name }} {
 			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
@@ -579,7 +551,6 @@ workflow {{ project_name }} {
 			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		
@@ -594,7 +565,6 @@ workflow {{ project_name }} {
 			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
@@ -611,7 +581,6 @@ workflow {{ project_name }} {
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,
 			dbsnp_dir=dbsnp_dir,
-			sample="LCL8",
 			docker=SENTIEONdocker,
 			disk_size=disk_size,
 			cluster_config=BIGcluster_config
@@ -624,7 +593,6 @@ workflow {{ project_name }} {
 			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