Merge branch 'dp-preemptible-cleanup' into dp-downsample

dpark01 · dpark01 · commit 449595bef006 · 2026-04-01T17:18:03.000-04:00
diff --git a/pipes/WDL/tasks/tasks_assembly.wdl b/pipes/WDL/tasks/tasks_assembly.wdl
@@ -196,7 +196,7 @@ task select_references {
     disks: "local-disk ~{disk_size} SSD"
     disk: "~{disk_size} GB" # TESs
     dx_instance_type: "mem1_ssd1_v2_x2"
-    preemptible: 2
+    preemptible: 3
   }
 }
 
@@ -858,7 +858,7 @@ task align_reads {
     disks: "local-disk ~{disk_size} LOCAL"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x8"
-    preemptible: 1
+    preemptible: 3
   }
 }
 
@@ -1125,7 +1125,6 @@ task run_discordance {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x2"
-        preemptible: 1
     }
 }
 
diff --git a/pipes/WDL/tasks/tasks_metagenomics.wdl b/pipes/WDL/tasks/tasks_metagenomics.wdl
@@ -336,7 +336,7 @@ task kraken2 {
     disks: "local-disk ~{disk_size} LOCAL"
     disk: "~{disk_size} GB" # TESs
     dx_instance_type: "mem3_ssd1_v2_x8"
-    preemptible: 2
+    preemptible: 3
   }
 }
 
@@ -384,7 +384,6 @@ task report_primary_kraken_taxa {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TESs
     dx_instance_type: "mem1_ssd1_v2_x2"
-    preemptible: 2
   }
 }
 
@@ -863,7 +862,7 @@ task filter_bam_to_taxa {
     disk: "~{disk_size} GB" # TES
     cpu: 8
     dx_instance_type: "mem1_ssd1_v2_x8"
-    preemptible: 1
+    preemptible: 3
   }
 }
 
diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
@@ -216,7 +216,6 @@ task plot_coverage {
     disks: "local-disk ~{disk_size} HDD"
     disk: "~{disk_size} GB" # TES
     dx_instance_type: "mem1_ssd1_v2_x4"
-    preemptible: 1
   }
 }
 
diff --git a/pipes/WDL/tasks/tasks_utils.wdl b/pipes/WDL/tasks/tasks_utils.wdl
@@ -356,7 +356,6 @@ task tar_extract {
         disks: "local-disk ~{disk_size} HDD"
         disk: "~{disk_size} GB" # TES
         dx_instance_type: "mem1_ssd1_v2_x2"
-        preemptible: 2
     }
     output {
         Array[File] files = glob("unpack/*")

Original file line number	Diff line number	Diff line change
`@@ -196,7 +196,7 @@ task select_references {`
`196`	`196`	`disks: "local-disk ~{disk_size} SSD"`
`197`	`197`	`disk: "~{disk_size} GB" # TESs`
`198`	`198`	`dx_instance_type: "mem1_ssd1_v2_x2"`
`199`		`- preemptible: 2`
	`199`	`+ preemptible: 3`
`200`	`200`	`}`
`201`	`201`	`}`
`202`	`202`
`@@ -858,7 +858,7 @@ task align_reads {`
`858`	`858`	`disks: "local-disk ~{disk_size} LOCAL"`
`859`	`859`	`disk: "~{disk_size} GB" # TES`
`860`	`860`	`dx_instance_type: "mem1_ssd1_v2_x8"`
`861`		`- preemptible: 1`
	`861`	`+ preemptible: 3`
`862`	`862`	`}`
`863`	`863`	`}`
`864`	`864`
`@@ -1125,7 +1125,6 @@ task run_discordance {`
`1125`	`1125`	`disks: "local-disk ~{disk_size} HDD"`
`1126`	`1126`	`disk: "~{disk_size} GB" # TES`
`1127`	`1127`	`dx_instance_type: "mem1_ssd1_v2_x2"`
`1128`		`- preemptible: 1`
`1129`	`1128`	`}`
`1130`	`1129`	`}`
`1131`	`1130`
Original file line number	Diff line number	Diff line change
`@@ -336,7 +336,7 @@ task kraken2 {`
`336`	`336`	`disks: "local-disk ~{disk_size} LOCAL"`
`337`	`337`	`disk: "~{disk_size} GB" # TESs`
`338`	`338`	`dx_instance_type: "mem3_ssd1_v2_x8"`
`339`		`- preemptible: 2`
	`339`	`+ preemptible: 3`
`340`	`340`	`}`
`341`	`341`	`}`
`342`	`342`
`@@ -384,7 +384,6 @@ task report_primary_kraken_taxa {`
`384`	`384`	`disks: "local-disk ~{disk_size} HDD"`
`385`	`385`	`disk: "~{disk_size} GB" # TESs`
`386`	`386`	`dx_instance_type: "mem1_ssd1_v2_x2"`
`387`		`- preemptible: 2`
`388`	`387`	`}`
`389`	`388`	`}`
`390`	`389`
`@@ -863,7 +862,7 @@ task filter_bam_to_taxa {`
`863`	`862`	`disk: "~{disk_size} GB" # TES`
`864`	`863`	`cpu: 8`
`865`	`864`	`dx_instance_type: "mem1_ssd1_v2_x8"`
`866`		`- preemptible: 1`
	`865`	`+ preemptible: 3`
`867`	`866`	`}`
`868`	`867`	`}`
`869`	`868`
Original file line number	Diff line number	Diff line change
`@@ -216,7 +216,6 @@ task plot_coverage {`
`216`	`216`	`disks: "local-disk ~{disk_size} HDD"`
`217`	`217`	`disk: "~{disk_size} GB" # TES`
`218`	`218`	`dx_instance_type: "mem1_ssd1_v2_x4"`
`219`		`- preemptible: 1`
`220`	`219`	`}`
`221`	`220`	`}`
`222`	`221`
Original file line number	Diff line number	Diff line change
`@@ -356,7 +356,6 @@ task tar_extract {`
`356`	`356`	`disks: "local-disk ~{disk_size} HDD"`
`357`	`357`	`disk: "~{disk_size} GB" # TES`
`358`	`358`	`dx_instance_type: "mem1_ssd1_v2_x2"`
`359`		`- preemptible: 2`
`360`	`359`	`}`
`361`	`360`	`output {`
`362`	`361`	`Array[File] files = glob("unpack/*")`