update

inputs

@@ -1,7 +1,7 @@
 {
   "{{ project_name }}.ref_dir": "oss://choppy-app-example-data/WGBS/hg38/",
   "{{ project_name }}.fastq_1": "{{ read1 }}",
-  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn2ne.2xlarge img-ubuntu-vpc' }}",
+  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
   "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/bismark:1.1.0_20190225",
   "{{ project_name }}.sample": "{{ sample_name }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}", 

tasks/Call_meth.wdl

@@ -1,6 +1,6 @@
 task Call_meth {
 	
-    File ref_dir
+	File ref_dir
     
 	File Dedup_bam
 	String sample
@@ -17,7 +17,7 @@ command <<<
 	runtime {
 		docker:docker
     	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
+    	systemDisk: "cloud_ssd 400"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 

tasks/Dedup.wdl

@@ -1,5 +1,5 @@
 task Dedup {
-	File unsorted_bam
+	File bam
 	String sample
 	String docker
 	String cluster_config
@@ -9,12 +9,12 @@ task Dedup {
 	command <<<
 		set -o pipefail
 		set -e
-		/src/Bismark-0.20.1/deduplicate_bismark -p --bam ${unsorted_bam} 
+		/src/Bismark-0.20.1/deduplicate_bismark -p --bam ${bam} 
 	>>>
 	runtime {
 		docker:docker
     		cluster: cluster_config
-    		systemDisk: "cloud_ssd 40"
+    		systemDisk: "cloud_ssd 500"
     		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 

tasks/Mapping.wdl

@@ -1,8 +1,8 @@
 task Mapping {
 
-    File ref_dir
-	File trim_read1
-	File trim_read2
+	File ref_dir
+	File fastq_1
+	File fastq_2
 
 	String sample
 	String docker
@@ -12,17 +12,17 @@ task Mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		/src/Bismark-0.20.1/bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${trim_read1} -2 ${trim_read2}
+		/src/Bismark-0.20.1/bismark --bowtie2 -p 8 --bam  ${ref_dir} -1 ${fastq_1} -2 ${fastq_2}
 
 	>>>
 
 	runtime {
 		docker:docker
     	cluster: cluster_config
-    	systemDisk: "cloud_ssd 40"
+    	systemDisk: "cloud_ssd 500"
     	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
-		File unsorted_bam = "${sample}_R1_bismark_bt2_pe.bam"
+		File bam = "${sample}_R1_bismark_bt2_pe.bam"
 	}
 }

workflow.wdl

@@ -16,22 +16,22 @@ workflow {{ project_name }} {
 	String disk_size
 	String cluster_config
 
-    File ref_dir
+	File ref_dir
 
 
 	call Mapping.Mapping as Mapping {
 		input: 
 		sample=sample,
 		ref_dir=ref_dir,
-		trim_read1=fastq_1,
-		trim_read2=fastq_2,
+		fastq_1=fastq_1,
+		fastq_2=fastq_2,
 		docker=docker,
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
 	call Dedup.Dedup as Dedup {
 		input:
-		unsorted_bam=Mapping.unsorted_bam,
+		bam=Mapping.bam,
 		sample=sample,
 		docker=docker,
 		disk_size=disk_size,