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revise-cluster-config

master
stead99 5 years ago
parent
commit
af25a3d538
3 changed files with 6 additions and 6 deletions
  1. +2
    -2
      tasks/arcashla.wdl
  2. +2
    -2
      tasks/hisat2.wdl
  3. +2
    -2
      tasks/samtools.wdl

+ 2
- 2
tasks/arcashla.wdl View File

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/"
} }

+ 2
- 2
tasks/hisat2.wdl View File

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/"
} }

+ 2
- 2
tasks/samtools.wdl View File

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/"
} }

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