Update 'input'

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
   "{{ project_name }}.fastq_1": "{{ fastq_1 }}",
   "{{ project_name }}.fastq_2": "{{ fastq_2 }}",
   "{{ project_name }}.normal_recaled_bam": "{{ normal_recaled_bam }}",

workflow.wdl

@@ -15,7 +15,7 @@ import "./tasks/vcf2maf.wdl" as vcf2maf
 
 workflow {{ project_name }} {
 	
-	String sample
+	String sample_id
 	File fastq_1
 	File fastq_2
 	File? normal_recaled_bam
@@ -51,8 +51,8 @@ workflow {{ project_name }} {
 
 	call mapping.mapping as mapping {
 		input: 
-		group=sample + '_' + type,
-		sample=sample + '_' + type,
+		group=sample_id + '_' + type,
+		sample=sample_id + '_' + type,
 		fastq_1=fastq_1,
 		fastq_2=fastq_2,
 		SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
@@ -73,7 +73,7 @@ workflow {{ project_name }} {
 		ref_dir=ref_dir,
 		sorted_bam=mapping.sorted_bam,
 		sorted_bam_index=mapping.sorted_bam_index,
-		sample=sample + '_' + type,
+		sample=sample_id + '_' + type,
 		docker=sentieon_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
@@ -85,7 +85,7 @@ workflow {{ project_name }} {
 		SENTIEON_LICENSE=SENTIEON_LICENSE,
 		sorted_bam=mapping.sorted_bam,
 		sorted_bam_index=mapping.sorted_bam_index,
-		sample=sample + '_' + type,
+		sample=sample_id + '_' + type,
 		docker=sentieon_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
@@ -99,7 +99,7 @@ workflow {{ project_name }} {
 		ref_dir=ref_dir,
 		Dedup_bam=Dedup.Dedup_bam,
 		Dedup_bam_index=Dedup.Dedup_bam_index,
-		sample=sample + '_' + type,
+		sample=sample_id + '_' + type,
 		docker=sentieon_docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
@@ -115,7 +115,7 @@ workflow {{ project_name }} {
 		Dedup_bam_index=Dedup.Dedup_bam_index,
 		db_mills=db_mills,
 		dbmills_dir=dbmills_dir,
-		sample=sample + '_' + type,
+		sample=sample_id + '_' + type,
 		docker=sentieon_docker,
 		disk_size=disk_size,
 		regions=regions,
@@ -134,7 +134,7 @@ workflow {{ project_name }} {
 		dbmills_dir=dbmills_dir,
 		dbsnp=dbsnp,
 		dbsnp_dir=dbsnp_dir,
-		sample=sample + '_' + type,
+		sample=sample_id + '_' + type,
 		regions=regions,
 		docker=sentieon_docker,
 		disk_size=disk_size,
@@ -146,7 +146,7 @@ workflow {{ project_name }} {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			sample=sample,
+			sample=sample_id,
 			fasta=fasta,
 			ref_dir=ref_dir,
 			normal_recaled_bam=BQSR.recaled_bam,
@@ -166,7 +166,7 @@ workflow {{ project_name }} {
 			input:
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
-			sample=sample,
+			sample=sample_id,
 			fasta=fasta,
 			ref_dir=ref_dir,
 			recaled_bam=BQSR.recaled_bam,
@@ -187,7 +187,7 @@ workflow {{ project_name }} {
 			SENTIEON_LICENSE=SENTIEON_LICENSE,
 			fasta=fasta,
 			ref_dir=ref_dir,
-			sample=sample,
+			sample=sample_id,
 			docker=sentieon_docker,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
@@ -219,10 +219,10 @@ workflow {{ project_name }} {
 			pon_vcf=pon_vcf,
 			cosmic_vcf=cosmic_vcf,
 			cosmic_dir=cosmic_dir,
-			tumor_name=sample + "_tumor",
-			normal_name=sample + "_normal",
+			tumor_name=sample_id + "_tumor",
+			normal_name=sample_id + "_normal",
 			docker=sentieon_docker,
-			sample=sample,
+			sample=sample_id,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 		}
@@ -243,10 +243,10 @@ workflow {{ project_name }} {
 			pon_vcf=pon_vcf,
 			cosmic_vcf=cosmic_vcf,
 			cosmic_dir=cosmic_dir,
-			tumor_name=sample + "_tumor",
-			normal_name=sample + "_normal",
+			tumor_name=sample_id + "_tumor",
+			normal_name=sample_id + "_normal",
 			docker=sentieon_docker,
-			sample=sample,
+			sample=sample_id,
 			disk_size=disk_size,
 			cluster_config=cluster_config
 		}
@@ -259,7 +259,7 @@ workflow {{ project_name }} {
 			database=database,
 			TNscope_vcf=TNscope.TNscope_vcf,
 			TNseq_vcf=TNseq.TNseq_vcf,
-			sample=sample,
+			sample=sample_id,
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
@@ -270,7 +270,7 @@ workflow {{ project_name }} {
 				docker=maftools_docker,
 				multianno_TNscope_txt=annovar.multianno_TNscope_txt,
 				multianno_TNseq_txt=annovar.multianno_TNseq_txt,
-				sample=sample,
+				sample=sample_id,
 				cluster_config=cluster_config,
 				disk_size=disk_size
 			}