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Add optional use of SSD in GenotypeBatch #924

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Add optional use of SSD in GenotypeBatch #924

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21f8c09
Add optional use of ssd in genotype batch.
VJalili Feb 26, 2026
bac8b39
undo .dockstore.yml
VJalili Feb 27, 2026
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28 changes: 20 additions & 8 deletions wdl/GenotypeBatch.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,8 @@ workflow GenotypeBatch {
RuntimeAttr? runtime_attr_genotype
RuntimeAttr? runtime_override_concat_shards
RuntimeAttr? runtime_attr_regeno_coverage_medians

Boolean use_ssd = false
}

call TrainSVGenotyping {
Expand All @@ -55,7 +57,8 @@ workflow GenotypeBatch {
pesr_exclusion_intervals_index = pesr_exclusion_intervals + ".tbi",
rf_cutoffs = rf_cutoffs,
gatk_docker = gatk_docker,
runtime_attr_override = runtime_attr_train
runtime_attr_override = runtime_attr_train,
use_ssd = use_ssd
}


Expand Down Expand Up @@ -83,7 +86,8 @@ workflow GenotypeBatch {
pe_table = TrainSVGenotyping.pe_table,
sr_table = TrainSVGenotyping.sr_table,
gatk_docker = gatk_docker,
runtime_attr_override = runtime_attr_genotype
runtime_attr_override = runtime_attr_genotype,
use_ssd = use_ssd
}
}

Expand All @@ -102,15 +106,17 @@ workflow GenotypeBatch {
vcf = ConcatVcfs.concat_vcf,
vcf_index = ConcatVcfs.concat_vcf_idx,
prefix = batch + ".genotype_batch",
sv_base_mini_docker = sv_base_mini_docker
sv_base_mini_docker = sv_base_mini_docker,
use_ssd = use_ssd
}

call GenerateRegenoCoverageMedians {
input:
vcf = SeparateDepthPesr.depth_vcf,
prefix = "~{batch}.regeno_coverage_medians",
sv_pipeline_docker = sv_pipeline_docker,
runtime_attr_override = runtime_attr_regeno_coverage_medians
runtime_attr_override = runtime_attr_regeno_coverage_medians,
use_ssd = use_ssd
}

output {
Expand Down Expand Up @@ -150,6 +156,8 @@ task TrainSVGenotyping {
String gatk_docker
Float? java_mem_fraction
RuntimeAttr? runtime_attr_override

Boolean use_ssd = false
}

RuntimeAttr default_attr = object {
Expand Down Expand Up @@ -205,7 +213,7 @@ task TrainSVGenotyping {
runtime {
cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + if use_ssd then " SSD" else " HDD"
bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
docker: gatk_docker
preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
Expand Down Expand Up @@ -239,6 +247,8 @@ task GenotypeSVs {
String gatk_docker
Float? java_mem_fraction
RuntimeAttr? runtime_attr_override

Boolean use_ssd = false
}

parameter_meta {
Expand Down Expand Up @@ -318,7 +328,7 @@ task GenotypeSVs {
runtime {
cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + if use_ssd then " SSD" else " HDD"
bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
docker: gatk_docker
preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
Expand All @@ -334,6 +344,7 @@ task SeparateDepthPesr {
String prefix
String sv_base_mini_docker
RuntimeAttr? runtime_attr_override
Boolean use_ssd = false
}

RuntimeAttr default_attr = object {
Expand Down Expand Up @@ -364,7 +375,7 @@ task SeparateDepthPesr {
runtime {
cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + if use_ssd then " SSD" else " HDD"
bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
docker: sv_base_mini_docker
preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
Expand All @@ -378,6 +389,7 @@ task SeparateDepthPesr {
String prefix
String sv_pipeline_docker
RuntimeAttr? runtime_attr_override
Boolean use_ssd = false
}

RuntimeAttr default_attr = object {
Expand Down Expand Up @@ -407,7 +419,7 @@ task SeparateDepthPesr {
runtime {
cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + if use_ssd then " SSD" else " HDD"
bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
docker: sv_pipeline_docker
preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
Expand Down