diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 662adb6f06..4ee8827c16 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -8,20 +8,20 @@ Glimpse2LowPassImputation 1.0.6 2026-08-12 Glimpse2LowPassImputationBatch 1.0.4 2026-08-12 Glimpse2LowPassImputationQC 1.0.5 2026-07-20 Glimpse2LowPassImputationQuotaConsumed 1.0.0 2026-06-30 -Glimpse2SVImputation 0.0.18 2026-08-13 -Glimpse2SVImputationBatch 0.0.13 2026-08-13 +Glimpse2SVImputation 0.0.19 2026-08-17 +Glimpse2SVImputationBatch 0.0.14 2026-08-17 IlluminaGenotypingArray 1.12.27 2026-01-21 Imputation 1.1.23 2025-10-03 ImputationBeagle 3.0.1 2026-02-23 JointGenotyping 1.7.3 2025-08-11 MultiSampleSmartSeq2SingleNucleus 2.2.8 2026-07-10 -MultilevelHierarchicallyPasteVcfsStreaming 0.0.5 2026-08-13 +MultilevelHierarchicallyPasteVcfsStreaming 0.0.6 2026-08-17 Multiome 7.0.2 2026-07-10 Optimus 9.2.0 2026-07-10 PairedTag 3.0.2 2026-07-10 PeakCalling 1.0.1 2025-08-11 Pipeline Name Version Date of Last Commit -PreprocessPLsGVCF 0.0.10 2026-08-13 +PreprocessPLsGVCF 0.0.11 2026-08-17 RNAWithUMIsPipeline 1.0.20 2026-01-21 ReblockGVCF 2.4.4 2026-01-29 SlideSeq 3.6.8 2026-07-10 diff --git a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.changelog.md b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.changelog.md index 060536de78..f96c239910 100644 --- a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.changelog.md +++ b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.changelog.md @@ -1,3 +1,9 @@ +# 0.0.19 +2026-08-17 (Date of Last Commit) + +* make all task disk sizes dynamic and set bootDiskSizeGb to 0 +* update default value of sample_batch_size to 1000 + # 0.0.18 2026-08-13 (Date of Last Commit) diff --git a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.wdl b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.wdl index 6251483f3f..0f20aff1b2 100644 --- a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.wdl +++ b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputation.wdl @@ -5,9 +5,9 @@ import "./Glimpse2SVImputationBatch.wdl" as Glimpse2SVImputationBatch import "../../../../tasks/wdl/Glimpse2SVImputationTasks.wdl" as Glimpse2SVImputationTasks workflow Glimpse2SVImputation { - String pipeline_version = "0.0.18" - String preprocess_pls_gvcf_pipeline_version = "0.0.10" - String batch_pipeline_version = "0.0.13" + String pipeline_version = "0.0.19" + String preprocess_pls_gvcf_pipeline_version = "0.0.11" + String batch_pipeline_version = "0.0.14" input { # if both array inputs and gvcf_manifest are provided, array inputs take precedence @@ -15,7 +15,7 @@ workflow Glimpse2SVImputation { Array[File]? input_gvcf_idxs Array[String]? sample_ids File? gvcf_manifest - Int sample_batch_size = 500 + Int sample_batch_size = 1000 String output_prefix diff --git a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.changelog.md b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.changelog.md index 0df107f505..d7db794860 100644 --- a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.changelog.md +++ b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.changelog.md @@ -1,3 +1,8 @@ +# 0.0.14 +2026-08-17 (Date of Last Commit) + +* make all task disk sizes dynamic and set bootDiskSizeGb to 0 + # 0.0.13 2026-08-13 (Date of Last Commit) diff --git a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.wdl b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.wdl index 6cd45b795b..88d415d781 100644 --- a/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.wdl +++ b/pipelines/wdl/glimpse/sv_imputation/Glimpse2SVImputationBatch.wdl @@ -4,7 +4,7 @@ import "../../../../tasks/wdl/Glimpse2SVImputationTasks.wdl" as Glimpse2SVImputa workflow Glimpse2SVImputationBatch { # if this changes, update the batch_pipeline_version value in Glimpse2SVImputation.wdl - String pipeline_version = "0.0.13" + String pipeline_version = "0.0.14" input { File input_preprocessed_joint_vcf @@ -167,7 +167,7 @@ task GLIMPSE2Phase { } } - Int disk_size_gb = ceil(size(input_vcf, "GiB") + size(panel_split_chunk_bin, "GiB") + size(genetic_map, "GiB") + 30) + Int disk_size_gb = ceil(size(input_vcf, "GiB") + size(panel_split_chunk_bin, "GiB") + size(genetic_map, "GiB") + 40) command <<< set -euxo pipefail @@ -211,7 +211,7 @@ task GLIMPSE2Phase { cpu_cores: threads, mem_gb: 16, disk_gb: disk_size_gb, - boot_disk_gb: 10, + boot_disk_gb: 0, use_ssd: true, preemptible_tries: 30, max_retries: 3, @@ -242,7 +242,7 @@ task GLIMPSE2Ligate { RuntimeAttr? runtime_attr_override } - Int disk_size_gb = 2 * ceil(size(phased_vcfs, "GB")) + 10 + Int disk_size_gb = ceil(2.1*size(phased_vcfs, "GB")) + 10 command <<< set -euox pipefail @@ -263,7 +263,7 @@ task GLIMPSE2Ligate { cpu_cores: 2, mem_gb: 18, disk_gb: disk_size_gb, - boot_disk_gb: 10, + boot_disk_gb: 0, use_ssd: true, preemptible_tries: 0, max_retries: 1, @@ -298,7 +298,7 @@ task PopAndMarginalizeCollisions { RuntimeAttr? runtime_attr_override } - Int disk_gb = 10 + 3 * ceil(size([posteriors_vcf, panel_bubble_split_sites_only_vcf, panel_id_split_vcf_gz], "GB")) + Int disk_gb = ceil(3*size(posteriors_vcf, "GB")) + ceil(size([panel_bubble_split_sites_only_vcf, panel_id_split_vcf_gz], "GB")) + 10 command <<< set -euox pipefail @@ -319,9 +319,9 @@ task PopAndMarginalizeCollisions { ######################### RuntimeAttr default_attr = object { cpu_cores: 2, - mem_gb: 6, + mem_gb: 8, disk_gb: disk_gb, - boot_disk_gb: 10, + boot_disk_gb: 0, use_ssd: true, preemptible_tries: 2, max_retries: 1, @@ -349,7 +349,7 @@ task UpdateHeader { Int mem_gb = 2 Int cpu = 1 - Int disk_size_gb = ceil(2.1 * size(bcf_to_reheader, "GiB") + 10) + Int disk_size_gb = ceil(2.1 * size(bcf_to_reheader, "GiB")) + 10 Int max_retries = 1 String docker } @@ -382,6 +382,7 @@ task UpdateHeader { runtime { docker: docker disks: "local-disk " + disk_size_gb + " SSD" + bootDiskSizeGb: 0 memory: mem_gb + " GiB" cpu: cpu maxRetries: max_retries diff --git a/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.changelog.md b/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.changelog.md index 369fc04bdf..11f0ed8338 100644 --- a/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.changelog.md +++ b/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.changelog.md @@ -1,3 +1,8 @@ +# 0.0.6 +2026-08-17 (Date of Last Commit) + +* make all task disk sizes dynamic and set bootDiskSizeGb to 0 + # 0.0.5 2026-08-13 (Date of Last Commit) diff --git a/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.wdl b/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.wdl index 1099442548..8dcc79ad73 100644 --- a/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.wdl +++ b/pipelines/wdl/glimpse/sv_imputation/MultilevelHierarchicallyPasteVcfsStreaming.wdl @@ -6,7 +6,7 @@ import "../../../../tasks/wdl/Glimpse2SVImputationTasks.wdl" as Glimpse2SVImputa workflow MultilevelHierarchicallyMergeVcfs { # if this changes, update the multi_level_paste_pipeline_version value in PreprocessPLsGVCF.wdl - String pipeline_version = "0.0.5" + String pipeline_version = "0.0.6" input { Array[String]? vcfs_array @@ -189,9 +189,9 @@ task CreateBatches { ######################### RuntimeAttr default_attr = object { cpu_cores: 1, - mem_gb: 4, + mem_gb: 2, disk_gb: 10, - boot_disk_gb: 10, + boot_disk_gb: 0, disk_type: "HDD", preemptible_tries: 2, max_retries: 1, @@ -226,7 +226,7 @@ task MergeVcfs { } # Dynamically sizes disk if localizing, defaults to 50GB if streaming - Int disk_gb = if length(vcfs_localize) > 0 then 10 + 2 * ceil(size(vcfs_localize, "GiB")) else 50 + Int disk_gb = if length(vcfs_localize) > 0 then ceil(2.1*size(vcfs_localize, "GiB")) + 10 else ceil(1.1*size(vcfs_localize, "GiB")) + 10 command <<< set -euox pipefail @@ -339,7 +339,7 @@ task MergeVcfs { cpu_cores: 2, mem_gb: 4, disk_gb: disk_gb, - boot_disk_gb: 10, + boot_disk_gb: 0, disk_type: "SSD", preemptible_tries: 3, max_retries: 0, diff --git a/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.changelog.md b/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.changelog.md index 8b961c249d..ac77795789 100644 --- a/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.changelog.md +++ b/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.changelog.md @@ -1,3 +1,8 @@ +# 0.0.11 +2026-08-17 (Date of Last Commit) + +* make all task disk sizes dynamic and set bootDiskSizeGb to 0 + # 0.0.10 2026-08-13 (Date of Last Commit) diff --git a/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.wdl b/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.wdl index 953ec3d4fb..043980c6b5 100644 --- a/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.wdl +++ b/pipelines/wdl/glimpse/sv_imputation/PreprocessPLsGVCF.wdl @@ -5,8 +5,8 @@ import "../../../../tasks/wdl/Glimpse2SVImputationTasks.wdl" as Glimpse2SVImputa workflow PreprocessPLsGVCF { # if this changes, update the preprocessing_pls_gvcf_pipeline_version value in Glimpse2SVImputation.wdl - String pipeline_version = "0.0.10" - String multi_level_paste_pipeline_version = "0.0.5" + String pipeline_version = "0.0.11" + String multi_level_paste_pipeline_version = "0.0.6" input { File input_gvcf_manifest @@ -85,7 +85,7 @@ task PreprocessPLs { RuntimeAttr? runtime_attr_override } - Int disk_size_gb = 10 + 2 * ceil(size([input_vcf, panel_bubble_split_sites_only_vcf], "GB")) + Int disk_size_gb = ceil(2*size([input_vcf, panel_bubble_split_sites_only_vcf], "GB")) + 10 File sample_names_list = write_lines(sample_names) @@ -116,7 +116,7 @@ task PreprocessPLs { cpu_cores: 1, mem_gb: 2, disk_gb: disk_size_gb, - boot_disk_gb: 10, + boot_disk_gb: 0, use_ssd: true, preemptible_tries: 4, max_retries: 1, diff --git a/tasks/wdl/Glimpse2SVImputationTasks.wdl b/tasks/wdl/Glimpse2SVImputationTasks.wdl index 3837c897a9..d24d19b166 100644 --- a/tasks/wdl/Glimpse2SVImputationTasks.wdl +++ b/tasks/wdl/Glimpse2SVImputationTasks.wdl @@ -75,6 +75,7 @@ task MergeSampleChunksVcfsWithPaste { runtime { docker: "us.gcr.io/broad-dsde-methods/bcftools_bgzip:beagle_imputation_v1.0.0" disks: "local-disk " + disk_size_gb + " HDD" + bootDiskSizeGb: 0 memory: mem_gb + " GiB" cpu: cpu preemptible: preemptible @@ -117,6 +118,7 @@ task ExtractAnnotations { runtime { docker: docker_extract_annotations disks: "local-disk " + disk_size_gb + " HDD" + bootDiskSizeGb: 0 memory: mem_gb + " GiB" cpu: cpu preemptible: preemptible @@ -210,6 +212,7 @@ EOF runtime { docker: docker_merge disks: "local-disk " + disk_size_gb + " HDD" + bootDiskSizeGb: 0 memory: mem_gb + " GiB" cpu: cpu preemptible: preemptible @@ -251,6 +254,7 @@ task CreateVcfIndexAndMd5 { runtime { docker: gatk_docker disks: "local-disk ${disk_size_gb} SSD" + bootDiskSizeGb: 0 memory: "${memory_mb} MiB" cpu: cpu preemptible: preemptible @@ -286,6 +290,7 @@ task FilterVcfByInfo { runtime { docker: docker disks: "local-disk " + disk_size_gb + " HDD" + bootDiskSizeGb: 0 memory: mem_gb + " GiB" cpu: cpu preemptible: preemptible @@ -340,6 +345,7 @@ task SplitVcfManifestIntoBatches { docker: "us.gcr.io/broad-dsde-methods/python-data-slim:1.0" cpu: 1 disks: "local-disk 10 HDD" + bootDiskSizeGb: 0 memory: "1 GiB" preemptible: 3 noAddress: true @@ -387,6 +393,7 @@ task ConvertInputArraysToManifest { cpu: 1 memory: "1 GiB" disks: "local-disk 10 HDD" + bootDiskSizeGb: 0 preemptible: 3 noAddress: true } @@ -430,8 +437,9 @@ task ParseVcfManifestIntoArrays { runtime { docker: "us.gcr.io/broad-dsde-methods/python-data-slim:1.0" cpu: 1 - memory: "4 GiB" + memory: "1 GiB" disks: "local-disk 10 HDD" + bootDiskSizeGb: 0 preemptible: 3 noAddress: true } @@ -472,7 +480,7 @@ task ConcatBcfs { cpu: 1 memory: "4 GiB" disks: "local-disk " + disk_gb + " SSD" - bootDiskSizeGb: 10 + bootDiskSizeGb: 0 preemptible: 3 maxRetries: 0 docker: "us.gcr.io/broad-gotc-prod/bcftools-vcftools:2.0.0-1.24-0.1.17-1784569943"