split fastq and vcf

tasks/filter_vcf.wdl

@@ -1,6 +1,6 @@
  task filter_vcf {
 	File vcf
-	String project
+	String sample = basename(vcf,".vcf")
 	String docker
 	String cluster_config
 	String disk_size
@@ -10,7 +10,7 @@
 		cat ${vcf} | grep '#' > header
 		cat ${vcf} | grep -v '#' > body
 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
-		cat header body.filtered > ${project}.filtered.vcf
+		cat header body.filtered > ${sample}.filtered.vcf
 	>>>
 
 	runtime {
@@ -20,6 +20,6 @@
 		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File filtered_vcf = "${project}.filtered.vcf"
+		File filtered_vcf = "${sample}.filtered.vcf"
 	}
 }

workflow.wdl

@@ -198,7 +198,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_D5 {
 			input:
 			vcf=Haplotyper_D5.vcf,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -344,7 +343,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_D6 {
 			input:
 			vcf=Haplotyper_D6.vcf,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -490,7 +488,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_F7 {
 			input:
 			vcf=Haplotyper_F7.vcf,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -636,7 +633,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_M8 {
 			input:
 			vcf=Haplotyper_M8.vcf,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -769,7 +765,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_D5_vcf {
 			input:
 			vcf=vcf_D5,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -789,7 +784,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_D6_vcf {
 			input:
 			vcf=vcf_D6,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -809,7 +803,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_F7_vcf {
 			input:
 			vcf=vcf_F7,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size			
@@ -829,7 +822,6 @@ workflow {{ project_name }} {
 		call filter_vcf.filter_vcf as filter_vcf_M8_vcf {
 			input:
 			vcf=vcf_M8,
-			project=project,
 			docker=BEDTOOLSdocker,
 			cluster_config=SMALLcluster_config,
 			disk_size=disk_size