{ | |||||
"{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc", | |||||
"{{ project_name }}.tar_file": "{{ tar_file }}", | |||||
"{{ project_name }}.disk_size": "200", | |||||
"{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4" | |||||
} |
task untar { | |||||
File tar_file | |||||
String docker | |||||
String cluster_config | |||||
String disk_size | |||||
command <<< | |||||
nt=$(nproc) | |||||
tar -zxvf ${tar_file} | |||||
>>> | |||||
runtime { | |||||
docker:docker | |||||
cluster: cluster_config | |||||
systemDisk: "cloud_ssd 40" | |||||
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | |||||
} | |||||
output { | |||||
Array[File] fastq_file = glob("*.fastq.gz") | |||||
} | |||||
} |
import "./tasks/untar.wdl" as untar | |||||
workflow {{ project_name }} { | |||||
File tar_file | |||||
String docker | |||||
String cluster_config | |||||
String disk_size | |||||
call untar.untar as untar { | |||||
input: | |||||
tar_file=tar_file, | |||||
docker=docker, | |||||
cluster_config=cluster_config, | |||||
disk_size=disk_size | |||||
} | |||||
} |