"{{ project_name }}.fq3": "{{ fq3 }}", | "{{ project_name }}.fq3": "{{ fq3 }}", | ||||
"{{ project_name }}.fq_m": "{{ fq_m }}", | "{{ project_name }}.fq_m": "{{ fq_m }}", | ||||
"{{ project_name }}.disk_size": "{{ disk_size }}", | "{{ project_name }}.disk_size": "{{ disk_size }}", | ||||
"{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1", | |||||
"{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc" | "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc" | ||||
} | } |
File fq3 | File fq3 | ||||
String fq_m | String fq_m | ||||
String disk_size | String disk_size | ||||
String docker | |||||
String cluster_config | String cluster_config | ||||
command <<< | command <<< | ||||
if [ ! ${fq3} ]; then | if [ ! ${fq3} ]; then | ||||
cat ${fq1} ${fq2} > ${fq_m} | cat ${fq1} ${fq2} > ${fq_m} | ||||
else | else | ||||
cat ${fq1} ${fq2} ${fq3} > ${fq_m} | |||||
cat ${fq1} ${fq2} ${fq3} > ${fq_m} | |||||
fi | fi | ||||
>>> | >>> | ||||
runtime { | runtime { | ||||
docker: docker | |||||
systemDisk: "cloud_ssd 40" | systemDisk: "cloud_ssd 40" | ||||
cluster: cluster_config | cluster: cluster_config | ||||
dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/" |
File? fq3 | File? fq3 | ||||
String fq_m | String fq_m | ||||
String disk_size | String disk_size | ||||
String docker | |||||
String cluster_config | String cluster_config | ||||
call mergefq.mergefq as mergefq { | call mergefq.mergefq as mergefq { |