Remove forced on-demand for GCP.

PacificBiosciences · Sep 28, 2023 · b99b12e · b99b12e
1 parent 2dc2760
commit b99b12e
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Showing 7 changed files with 5 additions and 39 deletions.
diff --git a/workflows/assemble_genome/assemble_genome.wdl b/workflows/assemble_genome/assemble_genome.wdl
@@ -17,24 +17,19 @@ workflow assemble_genome {
 
 		String backend
 		RuntimeAttributes default_runtime_attributes
-		RuntimeAttributes on_demand_runtime_attributes
 	}
 
-	# Preemptible jobs in GCP cannot live >24h; force on-demand for assembly in GCP
-	RuntimeAttributes assemble_runtime_attributes = if (backend == "GCP") then on_demand_runtime_attributes else default_runtime_attributes
-
 	call hifiasm_assemble {
 		input:
 			sample_id = sample_id,
 			reads_fastas = reads_fastas,
 			extra_params = hifiasm_extra_params,
 			father_yak = father_yak,
 			mother_yak = mother_yak,
-			runtime_attributes = assemble_runtime_attributes
+			runtime_attributes = default_runtime_attributes
 	}
 
 	scatter (gfa in hifiasm_assemble.assembly_hap_gfas) {
-		# Convert gfa to zipped fasta; calculate assembly stats
 		call gfa2fa {
 			input:
 				gfa = gfa,

diff --git a/workflows/assemble_genome/inputs.json b/workflows/assemble_genome/inputs.json
@@ -17,12 +17,5 @@
     "zones": "String",
     "queue_arn": "String",
     "container_registry": "String"
-  },
-  "assemble_genome.on_demand_runtime_attributes": {
-    "preemptible_tries": "Int",
-    "max_retries": "Int",
-    "zones": "String",
-    "queue_arn": "String",
-    "container_registry": "String"
   }
 }
diff --git a/workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl b/workflows/de_novo_assembly_sample/de_novo_assembly_sample.wdl
@@ -16,7 +16,6 @@ workflow de_novo_assembly_sample {
 
 		String backend
 		RuntimeAttributes default_runtime_attributes
-		RuntimeAttributes on_demand_runtime_attributes
 	}
 
 	scatter (movie_bam in sample.movie_bams) {
@@ -33,8 +32,7 @@ workflow de_novo_assembly_sample {
 			reads_fastas = samtools_fasta.reads_fasta,
 			references = references,
 			backend = backend,
-			default_runtime_attributes = default_runtime_attributes,
-			on_demand_runtime_attributes = on_demand_runtime_attributes
+			default_runtime_attributes = default_runtime_attributes
 	}
 
 	scatter (aln in assemble_genome.alignments) {
@@ -83,7 +81,6 @@ workflow de_novo_assembly_sample {
 		sample: {help: "Sample information and associated data files"}
 		references: {help: "Array of Reference genomes data"}
 		default_runtime_attributes: {help: "Default RuntimeAttributes; spot if preemptible was set to true, otherwise on_demand"}
-		on_demand_runtime_attributes: {help: "RuntimeAttributes for tasks that require dedicated instances"}
 	}
 }
 

diff --git a/workflows/de_novo_assembly_sample/inputs.json b/workflows/de_novo_assembly_sample/inputs.json
@@ -20,12 +20,5 @@
     "zones": "String",
     "queue_arn": "String",
     "container_registry": "String"
-  },
-  "de_novo_assembly_sample.on_demand_runtime_attributes": {
-    "preemptible_tries": "Int",
-    "max_retries": "Int",
-    "zones": "String",
-    "queue_arn": "String",
-    "container_registry": "String"
   }
 }
diff --git a/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl b/workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl
@@ -15,7 +15,6 @@ workflow de_novo_assembly_trio {
 
 		String backend
 		RuntimeAttributes default_runtime_attributes
-		RuntimeAttributes on_demand_runtime_attributes
 	}
 
 	call parse_families {
@@ -104,8 +103,7 @@ workflow de_novo_assembly_trio {
 					father_yak = yak_count_father.yak,
 					mother_yak = yak_count_mother.yak,
 					backend = backend,
-					default_runtime_attributes = default_runtime_attributes,
-					on_demand_runtime_attributes = on_demand_runtime_attributes
+					default_runtime_attributes = default_runtime_attributes
 			}
 		}
 	}
@@ -123,7 +121,6 @@ workflow de_novo_assembly_trio {
 		cohort: {help: "Sample information for the cohort"}
 		references: {help: "Array of Reference genomes data"}
 		default_runtime_attributes: {help: "Default RuntimeAttributes; spot if preemptible was set to true, otherwise on_demand"}
-		on_demand_runtime_attributes: {help: "RuntimeAttributes for tasks that require dedicated instances"}
 	}
 }
 

diff --git a/workflows/de_novo_assembly_trio/inputs.json b/workflows/de_novo_assembly_trio/inputs.json
@@ -26,12 +26,5 @@
     "zones": "String",
     "queue_arn": "String",
     "container_registry": "String"
-  },
-  "de_novo_assembly_trio.on_demand_runtime_attributes": {
-    "preemptible_tries": "Int",
-    "max_retries": "Int",
-    "zones": "String",
-    "queue_arn": "String",
-    "container_registry": "String"
   }
 }
diff --git a/workflows/main.wdl b/workflows/main.wdl
@@ -40,8 +40,7 @@ workflow de_novo_assembly {
 					sample = sample,
 					references = references,
 					backend = backend,
-					default_runtime_attributes = default_runtime_attributes,
-					on_demand_runtime_attributes = backend_configuration.on_demand_runtime_attributes
+					default_runtime_attributes = default_runtime_attributes
 			}
 		}
 	}
@@ -53,8 +52,7 @@ workflow de_novo_assembly {
 					cohort = cohort,
 					references = references,
 					backend = backend,
-					default_runtime_attributes = default_runtime_attributes,
-					on_demand_runtime_attributes = backend_configuration.on_demand_runtime_attributes
+					default_runtime_attributes = default_runtime_attributes
 			}
 		}
 	}