diff --git a/CNV-Profiler/CNV-Profiler.wdl b/CNV-Profiler/CNV-Profiler.wdl index 8dc0a22..79dad90 100644 --- a/CNV-Profiler/CNV-Profiler.wdl +++ b/CNV-Profiler/CNV-Profiler.wdl @@ -153,9 +153,10 @@ task SamtoolsDepth { File target_bed Int minBaseQuality = 20 Int minMappingQuality = 20 - Int? mem_gb - Int? cpu - Int? disk_size_gb + Int mem_gb = 32 + Int cpu = 4 + Int disk_size_gb = 500 + Boolean use_ssd = true String samtools_docker = "euformatics/samtools:1.20" } command <<< @@ -179,10 +180,10 @@ task SamtoolsDepth { File depth_profile = "output/~{sampleName}_samtools.depth" } runtime { - memory: select_first([mem_gb, 7]) * 1000 + " MB" - cpu: select_first([cpu, 1]) + memory: mem_gb * 1000 + " MB" + cpu: cpu docker: samtools_docker - disks: "local-disk ~{disk_size_gb} SSD" + disks: "local-disk " + disk_size_gb + if use_ssd then " SSD" else " HDD" preemptible: 0 maxRetries: 3 } @@ -199,6 +200,7 @@ task cnvDepthProfiler{ Int preemptible = 0 Int disk_size_gb = 500 Int maxRetries = 1 + Boolean use_ssd = true } command <<< set -e @@ -220,7 +222,7 @@ task cnvDepthProfiler{ memory: mem_gb + " GB" cpu: cpu docker: cnvProfiler_Docker - disks: "local-disk ~{disk_size_gb} SSD" + disks: "local-disk " + disk_size_gb + if use_ssd then " SSD" else " HDD" preemptible: preemptible maxRetries: maxRetries } @@ -239,6 +241,7 @@ task HeterozygosityCheck{ Int preemptible = 0 Int disk_size_gb = 500 Int maxRetries = 1 + Boolean use_ssd = true } command <<< set -e @@ -265,7 +268,7 @@ task HeterozygosityCheck{ memory: mem_gb + " GB" cpu: cpu docker: cnvProfiler_Docker - disks: "local-disk ~{disk_size_gb} SSD" + disks: "local-disk " + disk_size_gb + if use_ssd then " SSD" else " HDD" preemptible: preemptible maxRetries: maxRetries }