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tpshea2claude
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Tune HifiKraken2 runtime: 160 GB, preemptible:3, SSD
hash.k2d for k2_pluspf_20250714 is 113 GB; 160 GB gives 40 GB headroom and improves spot VM availability vs 180 GB. SSD cuts the 120 GB archive extraction from ~15 min to ~2 min, reducing the preemption exposure window. preemptible:3 + max_retries:1 matches viral-pipelines convention (3 spot attempts, 1 non-preemptible fallback). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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wdl/tasks/QC/HifiQC.wdl

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -315,18 +315,18 @@ task HifiKraken2 {
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#########################
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RuntimeAttr default_attr = object {
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cpu_cores: 8,
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mem_gb: 180,
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mem_gb: 160,
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disk_gb: disk_size,
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boot_disk_gb: 25,
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preemptible_tries: 2,
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preemptible_tries: 3,
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max_retries: 1,
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docker: "ghcr.io/broadinstitute/hvp-lr/hvp-monolith:0.0.3"
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}
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RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
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runtime {
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cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])
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memory: select_first([runtime_attr.mem_gb, default_attr.mem_gb]) + " GiB"
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disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " HDD"
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disks: "local-disk " + select_first([runtime_attr.disk_gb, default_attr.disk_gb]) + " SSD"
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bootDiskSizeGb: select_first([runtime_attr.boot_disk_gb, default_attr.boot_disk_gb])
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preemptible: select_first([runtime_attr.preemptible_tries, default_attr.preemptible_tries])
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maxRetries: select_first([runtime_attr.max_retries, default_attr.max_retries])

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