inputs

inputs

@@ -4,7 +4,7 @@
   "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
-  "{{ project_name }}.project_name": "{{ project_name }}",
+  "{{ project_name }}.project": "{{ project }}",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
   "{{ project_name }}.ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
 }

tasks/GVCFtyper.wdl

@@ -5,7 +5,7 @@ task GVCFtyper {
 	String fasta
 	Array[File] vcf
 	Array[File] vcf_idx
-	String project_name
+	String project
 	String docker
 	String cluster_config
 	String disk_size
@@ -15,7 +15,7 @@ command <<<
 		set -e
 		export SENTIEON_LICENSE=192.168.0.55:8990
 		nt=$(nproc)	
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project_name}.joint.g.vcf ${sep=" " vcf}
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} --algo GVCFtyper ${project}.joint.g.vcf ${sep=" " vcf}
 	>>>
 	
 	runtime {
@@ -26,8 +26,8 @@ command <<<
 	}
 
 	output {
-		File gvcf = "${project_name}.joint.g.vcf"
-		File gvcf_idx = "${project_name}.joint.g.vcf.idx"
+		File gvcf = "${project}.joint.g.vcf"
+		File gvcf_idx = "${project}.joint.g.vcf.idx"
 	}
 }
 

workflow.wdl

@@ -1,14 +1,14 @@
 import "./tasks/gVCF_chromo_split.wdl" as gVCF_chromo_split
 import "./tasks/GVCFtyper.wdl" as GVCFtyper
 
-workflow {{ project_name }} {
+workflow project_name {
 
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 
 	String SENTIEON_INSTALL_DIR
 	String docker
-	String project_name
+	String project
 	String fasta
 	File ref_dir
 	String disk_size
@@ -33,7 +33,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr1_gvcf,
 		vcf_idx=gVCF_chromo_split.chr1_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -45,7 +45,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr2_gvcf,
 		vcf_idx=gVCF_chromo_split.chr2_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -57,7 +57,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr3_gvcf,
 		vcf_idx=gVCF_chromo_split.chr3_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -69,7 +69,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr4_gvcf,
 		vcf_idx=gVCF_chromo_split.chr4_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -81,7 +81,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr5_gvcf,
 		vcf_idx=gVCF_chromo_split.chr5_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -93,7 +93,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr6_gvcf,
 		vcf_idx=gVCF_chromo_split.chr6_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -105,7 +105,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr7_gvcf,
 		vcf_idx=gVCF_chromo_split.chr7_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -117,7 +117,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr8_gvcf,
 		vcf_idx=gVCF_chromo_split.chr8_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -129,7 +129,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr9_gvcf,
 		vcf_idx=gVCF_chromo_split.chr9_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -141,7 +141,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr10_gvcf,
 		vcf_idx=gVCF_chromo_split.chr10_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -153,7 +153,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr11_gvcf,
 		vcf_idx=gVCF_chromo_split.chr11_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -165,7 +165,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr12_gvcf,
 		vcf_idx=gVCF_chromo_split.chr12_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -177,7 +177,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr13_gvcf,
 		vcf_idx=gVCF_chromo_split.chr13_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -189,7 +189,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr14_gvcf,
 		vcf_idx=gVCF_chromo_split.chr14_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -201,7 +201,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr15_gvcf,
 		vcf_idx=gVCF_chromo_split.chr15_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -213,7 +213,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr16_gvcf,
 		vcf_idx=gVCF_chromo_split.chr16_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -225,7 +225,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr17_gvcf,
 		vcf_idx=gVCF_chromo_split.chr17_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -237,7 +237,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr18_gvcf,
 		vcf_idx=gVCF_chromo_split.chr18_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -249,7 +249,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr19_gvcf,
 		vcf_idx=gVCF_chromo_split.chr19_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -261,7 +261,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr20_gvcf,
 		vcf_idx=gVCF_chromo_split.chr20_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -273,7 +273,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr21_gvcf,
 		vcf_idx=gVCF_chromo_split.chr21_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -285,7 +285,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chr22_gvcf,
 		vcf_idx=gVCF_chromo_split.chr22_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -297,7 +297,7 @@ workflow {{ project_name }} {
 		fasta=fasta,
 		vcf=gVCF_chromo_split.chrX_gvcf,
 		vcf_idx=gVCF_chromo_split.chrX_gvcf_idx,
-		project_name=project_name,
+		project=project,
 		docker=docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size