File bam | File bam | ||||
String base = basename(bam, ".sorted.bam") | String base = basename(bam, ".sorted.bam") | ||||
String docker | String docker | ||||
String cluster | |||||
String cluster_config | |||||
String disk_size | String disk_size | ||||
command <<< | command <<< | ||||
runtime { | runtime { | ||||
docker: docker | docker: docker | ||||
cluster: cluster | |||||
cluster: cluster_config | |||||
systemDisk: "cloud_ssd 40" | systemDisk: "cloud_ssd 40" | ||||
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | ||||
} | } |
String idx_prefix | String idx_prefix | ||||
String base = sub(basename(read_1P),"\\.\\S+$", "") | String base = sub(basename(read_1P),"\\.\\S+$", "") | ||||
String docker | String docker | ||||
String cluster | |||||
String cluster_config | |||||
String disk_size | String disk_size | ||||
command { | command { | ||||
runtime { | runtime { | ||||
docker: docker | docker: docker | ||||
cluster: cluster | |||||
cluster: cluster_config | |||||
systemDisk: "cloud_ssd 40" | systemDisk: "cloud_ssd 40" | ||||
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | ||||
} | } |
String sorted_bam = base + ".sorted.bam" | String sorted_bam = base + ".sorted.bam" | ||||
String sorted_bam_index = base + ".sorted.bam.bai" | String sorted_bam_index = base + ".sorted.bam.bai" | ||||
String docker | String docker | ||||
String cluster | |||||
String cluster_config | |||||
String disk_size | String disk_size | ||||
command <<< | command <<< | ||||
runtime { | runtime { | ||||
docker: docker | docker: docker | ||||
cluster: cluster | |||||
cluster: cluster_config | |||||
systemDisk: "cloud_ssd 40" | systemDisk: "cloud_ssd 40" | ||||
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/" | ||||
} | } |