From b99b12ecd5bef8cb8acc7972260728b0c7ff511e Mon Sep 17 00:00:00 2001 From: William Rowell Date: Thu, 28 Sep 2023 13:45:02 -0700 Subject: [PATCH] Remove forced on-demand for GCP. --- workflows/assemble_genome/assemble_genome.wdl | 7 +------ workflows/assemble_genome/inputs.json | 7 ------- .../de_novo_assembly_sample/de_novo_assembly_sample.wdl | 5 +---- workflows/de_novo_assembly_sample/inputs.json | 7 ------- workflows/de_novo_assembly_trio/de_novo_assembly_trio.wdl | 5 +---- workflows/de_novo_assembly_trio/inputs.json | 7 ------- workflows/main.wdl | 6 ++---- 7 files changed, 5 insertions(+), 39 deletions(-) diff --git a/workflows/assemble_genome/assemble_genome.wdl b/workflows/assemble_genome/assemble_genome.wdl index 1e6807f..78c685f 100644 --- a/workflows/assemble_genome/assemble_genome.wdl +++ b/workflows/assemble_genome/assemble_genome.wdl @@ -17,12 +17,8 @@ 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, @@ -30,11 +26,10 @@ workflow assemble_genome { 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 index 6c8fbe8..29e5993 100644 --- 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 index 43354fc..2344114 100644 --- 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 index cf72f36..57d9877 100644 --- 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 index 5db4c29..06bb020 100644 --- 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 index 3aacd62..306682f 100644 --- 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 index 7647f34..062ed79 100644 --- 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 } } }