diff --git a/CramToBam/CramToBam.wdl b/CramToBam/CramToBam.wdl index 7b47dc0..c6c74d2 100644 --- a/CramToBam/CramToBam.wdl +++ b/CramToBam/CramToBam.wdl @@ -51,9 +51,9 @@ workflow CramToBamWorkflow { File cram_file String sample_id String docker_image = "broadinstitute/genomes-in-the-cloud:2.3.1-1504795437" - Int? mem_size - Int? disk_size - Int? preemptible_attempts + Int? mem_size = 32 + Int? disk_size = 500 + Int? preemptible_attempts = 2 } command <<< set -e @@ -74,9 +74,9 @@ workflow CramToBamWorkflow { } runtime { docker: docker_image - memory: select_first([mem_size, 4]) + " GB" - disks: "local-disk " + select_first([disk_size, 200]) + " HDD" - preemptible: select_first([preemptible_attempts, 2]) + memory: mem_size + " GB" + disks: "local-disk " + disk_size + " HDD" + preemptible: preemtible_attempts } } @@ -87,9 +87,9 @@ workflow CramToBamWorkflow { String sample_id String gatk_docker = "broadinstitute/gatk:4.6.0.0" String output_mode = "SUMMARY" - Int? mem_size - Int? disk_size - Int? preemptible_attempts + Int? mem_size = 32 + Int? disk_size = 500 + Int? preemptible_attempts = 2 } Int machine_mem_mb = select_first([mem_size, 7]) * 1000 Int command_mem_mb = machine_mem_mb - 1000 @@ -104,9 +104,9 @@ workflow CramToBamWorkflow { } runtime { docker: gatk_docker - memory: select_first([mem_size, 4]) + " GB" - disks: "local-disk " + select_first([disk_size, 100]) + " HDD" - preemptible: select_first([preemptible_attempts, 2]) + memory: mem_size + " GB" + disks: "local-disk " + disk_size + " HDD" + preemptible: preemtible_attempts } -} \ No newline at end of file +}