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expose disk_space_gb for long-running augur tasks; raise default 375 -> 750 #89

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merged 2 commits into from
May 29, 2020
Merged

expose disk_space_gb for long-running augur tasks; raise default 375 -> 750 #89

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expose disk_space_gb for long-running augur tasks; raise default 375 …
tomkinsc May 28, 2020
beffca8
Merge branch 'master' into ct-expose_disk_space_gb
tomkinsc May 29, 2020
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9 changes: 6 additions & 3 deletions pipes/WDL/tasks/tasks_nextstrain.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -152,6 +152,7 @@ task augur_mafft_align {
Boolean remove_reference = true

Int? machine_mem_gb
Int? disk_space_gb = 750
String docker = "nextstrain/base"
}
command {
Expand All @@ -170,7 +171,7 @@ task augur_mafft_align {
docker: docker
memory: select_first([machine_mem_gb, 104]) + " GB"
cpu : 16
disks: "local-disk 375 LOCAL"
disks: "local-disk ${disk_space_gb} LOCAL"
preemptible: 0
dx_instance_type: "mem3_ssd2_v2_x16"
}
Expand All @@ -196,6 +197,7 @@ task draft_augur_tree {
String? tree_builder_args

Int? machine_mem_gb
Int? disk_space_gb = 750
String docker = "nextstrain/base"
}
command {
Expand All @@ -213,7 +215,7 @@ task draft_augur_tree {
docker: docker
memory: select_first([machine_mem_gb, 30]) + " GB"
cpu : 16
disks: "local-disk 375 LOCAL"
disks: "local-disk ${disk_space_gb} LOCAL"
dx_instance_type: "mem1_ssd1_v2_x16"
preemptible: 0
}
Expand Down Expand Up @@ -250,6 +252,7 @@ task refine_augur_tree {
File? vcf_reference

Int? machine_mem_gb
Int? disk_space_gb = 750
String docker = "nextstrain/base"
}
command {
Expand Down Expand Up @@ -281,7 +284,7 @@ task refine_augur_tree {
docker: docker
memory: select_first([machine_mem_gb, 30]) + " GB"
cpu : 16
disks: "local-disk 375 LOCAL"
disks: "local-disk ${disk_space_gb} LOCAL"
dx_instance_type: "mem1_ssd1_v2_x16"
preemptible: 0
}
Expand Down