first commit

defaults

+{
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "disk_size": "200"
+}

inputs

+{
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.fastq": "{{ fastq }}",
+  "{{ project_name }}.p": "{{ p }}",
+  "{{ project_name }}.docker_seqkit": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/seqkit:0.12.0",
+  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}
+

tasks/DownSample.wdl

+task DownSample {
+
+  String sample_id
+  File fastq
+  Float p
+  String docker_seqkit
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    seqkit sample --two-pass -s 100 -p ${p} ${fastq} -o ${sample_id}.fastq.gz
+  >>>
+
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  output {
+    File out_fastq = "${sample_id}.fastq.gz"
+  }
+
+}

workflow.wdl

+import "./tasks/DownSample.wdl" as DownSample
+
+workflow {{ project_name }} {
+  
+  String sample_id
+  File fastq
+  Float p
+  String docker_seqkit
+  String cluster_config
+  String disk_size
+
+  call DownSample.DownSample as DownSample {
+    input:
+      sample_id=sample_id,
+      fastq=fastq,
+      p=p,
+      docker=docker_seqkit,
+      cluster_config=cluster_config,
+      disk_size=disk_size
+  }
+}