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Sz add mem disk aligned metrics #448

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Sz add mem disk aligned metrics #448

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f6f512f
Modify ReadMetrics task with customizable memory and SSD support
shadizaheri Apr 23, 2024
c76413b
Modify AlignedMetrics inputs with customizable memory and SSD support
shadizaheri Apr 23, 2024
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14 changes: 10 additions & 4 deletions wdl/tasks/QC/AlignedMetrics.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,10 @@ workflow AlignedMetrics {
File ref_dict

String? gcs_output_dir

Int? mem_gb_input_ReadMetrics # Optional input for memory in GiB
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Actually, it might be better to define the inputs as the struct for runtime attributes. Then you can just bubble that whole struct down.

RuntimeAttr? runtime_attr_override

Int? disk_gb_input_ReadMetrics # Optional input for disk size in GiB

}

call ReadMetrics as AlignedReadMetrics { input: bam = aligned_bam }
Expand Down Expand Up @@ -625,12 +629,14 @@ task ComputeBedCoverage {
task ReadMetrics {
input {
File bam

Int? mem_gb_input_ReadMetrics # Optional input for memory in GiB
Int? disk_gb_input_ReadMetrics # Optional input for disk size in GiB
RuntimeAttr? runtime_attr_override
}

String basename = basename(bam, ".bam")
Int disk_size = 2*ceil(size(bam, "GB"))
Int calculated_disk_size = 2*ceil(size(bam, "GB"))
Int disk_size = select_first([disk_gb_input_ReadMetrics, calculated_disk_size]) # Use disk_gb_input if provided, otherwise use calculated_disk_size

command <<<
set -euxo pipefail
Expand All @@ -655,8 +661,8 @@ task ReadMetrics {
#########################
RuntimeAttr default_attr = object {
cpu_cores: 2,
mem_gb: 50,
disk_gb: disk_size,
mem_gb: select_first([mem_gb_input_ReadMetrics, 50]), # Use mem_gb_input if provided, otherwise default to 50
disk_gb: disk_size, # Use disk_gb_input if provided, otherwise use calculated_disk_size
boot_disk_gb: 10,
preemptible_tries: 2,
max_retries: 1,
Expand Down