Skip to content

fix: uses Int instead of String for cpu runtime values #1811

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
claymcleod wants to merge 1 commit into
base: develop
Choose a base branch
from
Open

fix: uses Int instead of String for cpu runtime values #1811

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions all_of_us/PCA/pca_only_no_labels.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ task ConcatenateChromosomalVcfs {
runtime {
docker: bcftools_docker
memory: "${memory_gb} GB"
cpu: "${cpu}"
cpu: cpu
disk: "local-disk ${disk_gb} HDD"
preemptible: num_preemptible_attempts
}
Expand Down Expand Up @@ -155,7 +155,7 @@ task create_hw_pca_training {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "${mem_gb} GB"
cpu: "${cpu}"
cpu: cpu
disks: "local-disk ${disk_gb} ${disk_type}" # large SSD is recommended for increased processing speed
}
}
Expand Down Expand Up @@ -244,7 +244,7 @@ task plot_pca {
runtime {
docker: "faizanbashir/python-datascience:3.6"
memory: "${mem_gb} GB"
cpu: "${cpu}"
cpu: cpu
disks: "local-disk ${disk_gb} HDD"
}
}
8 changes: 4 additions & 4 deletions all_of_us/ancestry/determine_hq_sites_intersection.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@ task sitesOnlyAndHQFilterVcf {
runtime {
docker:"us.gcr.io/broad-gatk/gatk:4.2.0.0"
memory: "12 GB"
cpu: "4"
cpu: 4
disks: "local-disk 100 HDD"
}
}
Expand Down Expand Up @@ -244,7 +244,7 @@ task merge_vcf_bgzs {
runtime {
docker: "mgibio/bcftools-cwl:1.12"
memory: "120 GB"
cpu: "16"
cpu: 16
disks: "local-disk 1500 HDD"
bootDiskSizeGb: 1500
}
Expand Down Expand Up @@ -303,7 +303,7 @@ task filter_by_sites_only {
runtime {
docker:"us.gcr.io/broad-gatk/gatk:4.2.0.0"
memory: "7 GB"
cpu: "1"
cpu: 1
disks: "local-disk 100 HDD"
}
}
Expand Down Expand Up @@ -340,7 +340,7 @@ task intersect_vcfs_as_sites_only {
runtime {
docker: "us.gcr.io/broad-gatk/gatk:4.2.0.0"
memory: "7 GB"
cpu: "1"
cpu: 1
disks: "local-disk 500 HDD"
}
}
6 changes: 3 additions & 3 deletions all_of_us/ancestry/run_ancestry.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,7 @@ task create_hw_pca_training {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "123 GB"
cpu: "4"
cpu: 4
disks: "local-disk 500 HDD"
}
}
Expand Down Expand Up @@ -280,7 +280,7 @@ task call_ancestry {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "240 GB"
cpu: "4"
cpu: 4
disks: "local-disk 700 HDD"
}
}
Expand Down Expand Up @@ -377,7 +377,7 @@ task plot_ancestry {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "7 GB"
cpu: "4"
cpu: 4
disks: "local-disk 100 HDD"
}
}
4 changes: 2 additions & 2 deletions all_of_us/ancestry/run_sample_outlier_qc.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ task join_ancestry_to_stats {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "15 GB"
cpu: "2"
cpu: 2
disks: "local-disk 500 HDD"
}
}
Expand Down Expand Up @@ -187,7 +187,7 @@ task determine_outlier_qc {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "15 GB"
cpu: "4"
cpu: 4
disks: "local-disk 500 HDD"
}
}
Expand Down
6 changes: 3 additions & 3 deletions all_of_us/ancestry/run_sample_outlier_qc_plotting.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,7 @@ task join_ancestry_to_demographics {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "7 GB"
cpu: "4"
cpu: 4
disks: "local-disk 100 HDD"
}
}
Expand Down Expand Up @@ -144,7 +144,7 @@ task plot_first_pcs {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "7 GB"
cpu: "4"
cpu: 4
disks: "local-disk 100 HDD"
}
}
Expand Down Expand Up @@ -246,7 +246,7 @@ task plot_metrics_and_fitting {
runtime {
docker: "hailgenetics/hail:0.2.67"
memory: "26 GB"
cpu: "4"
cpu: 4
disks: "local-disk 100 HDD"
}
}
2 changes: 1 addition & 1 deletion all_of_us/pgx/CyriusStarAlleleCalling.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ task PrintReads {
docker: "us.gcr.io/broad-gotc-prod/gatk:1.3.0-4.2.6.1-1649964384"
preemptible: preemptible_tries
memory: "10000 MiB"
cpu: "1"
cpu: 1
disks: "local-disk " + disk_size + " HDD"
}
output {
Expand Down
2 changes: 1 addition & 1 deletion all_of_us/pgx/StargazerFromJointVCF.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ task SelectVariants {
>>>
runtime {
memory: "7 GB"
cpu: "1"
cpu: 1
disks: "local-disk " + disk_size + " HDD"
docker: "us.gcr.io/broad-gatk/gatk:4.4.0.0"
}
Expand Down
4 changes: 2 additions & 2 deletions all_of_us/rna_seq/AggregateSusieWorkflow.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ task AggregateSusie{
docker: "ghcr.io/aou-multiomics-analysis/aggregate_susie:main@sha256:ede17b5112eadb765f22cdfbd2a987da96087a1e2f0ad224994c16f1af645443"
disks: "local-disk 500 SSD"
memory: "~{Memory}GB"
cpu: "~{NumThreads}"
cpu: NumThreads
}


Expand Down Expand Up @@ -77,7 +77,7 @@ task AnnotateSusie {
docker: "ghcr.io/aou-multiomics-analysis/aggregate_susie:main@sha256:ede17b5112eadb765f22cdfbd2a987da96087a1e2f0ad224994c16f1af645443"
disks: "local-disk 500 SSD"
memory: "~{Memory}GB"
cpu: "1"
cpu: 1
}


Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/CalculatePhenotypeGroups.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ task PrepareSpliceData {
docker: "ghcr.io/aou-multiomics-analysis/prepare_qtl@sha256:b9986a803ad82aee02945e9131f180fc028c73eadb889184e23aff8dabf573fe"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${num_threads}"
cpu: num_threads
}

output {
Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/GTEx/aggregate_rsem_results.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,7 @@ task rsem_aggregate_results {
docker: "gcr.io/broad-cga-francois-gtex/gtex_rnaseq:V10"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${num_threads}"
cpu: num_threads
preemptible: "${num_preempt}"
}

Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/leafcutter_bam_to_junc.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ task leafcutter_bam_to_junc {
docker: "gcr.io/broad-cga-francois-gtex/leafcutter:latest"
memory: "~{memory}GB"
disks: "local-disk ~{disk_space} HDD"
cpu: "~{num_threads}"
cpu: num_threads
preemptible: "~{num_preempt}"
}

Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/leafcutter_cluster.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ task leafcutter_cluster {
docker: "us.gcr.io/broad-gotc-prod/leafcutter:1.0.0"
memory: "~{memory}GB"
disks: "local-disk ~{disk_space} HDD"
cpu: "~{num_threads}"
cpu: num_threads
preemptible: "~{num_preempt}"
}

Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/prepare_QTL/calculateAF.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ workflow CaclulateAF {
docker: "quay.io/biocontainers/plink2:2.0.0a.6.9--h9948957_0"
memory: "~{memory}GB"
disks: "local-disk ~{disk_space} HDD"
cpu: "~{num_threads}"
cpu: num_threads

}

Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/prepare_QTL/calculateGenotypeDosage.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ task BcftoolsDosage {
runtime {
docker: "quay.io/eqtlcatalogue/susie-finemapping:v20.08.1"
memory: "32G"
cpu: "${threads}"
cpu: threads
disks: "local-disk 500 SSD"
}

Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/prepare_QTL/calculate_phenotypePCs.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ task ComputePCs{
docker: "us.gcr.io/broad-gotc-prod/aou_rna_prepareqtl:0.0.1"
memory: "~{memory}GB"
disks: "local-disk ~{disk_space} HDD"
cpu: "~{num_threads}"
cpu: num_threads
}

output {
Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/prepare_QTL/prepare_eQTL.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ task eqtl_prepare_expression {
docker: "us.gcr.io/broad-gotc-prod/aou_rna_prepareqtl:0.0.1"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${num_threads}"
cpu: num_threads
}

output {
Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/prepare_QTL/prepare_sQTL.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ task PrepareSpliceData {
docker: "us.gcr.io/broad-gotc-prod/aou_rna_prepareqtl:0.0.1"
memory: "${memory}GB"
disks: "local-disk ${disk_space} HDD"
cpu: "${num_threads}"
cpu: num_threads
}

output {
Expand Down
4 changes: 2 additions & 2 deletions all_of_us/rna_seq/susieR_workflow.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ task PrepInputs {
disks: "local-disk 500 SSD"
preemptible: "${NumPrempt}"
memory: "2GB"
cpu: "1"
cpu: 1
}

output {
Expand Down Expand Up @@ -121,7 +121,7 @@ task susieR {
disks: "local-disk 500 SSD"
bootDiskSizeGb: 25
preemptible: "${NumPrempt}"
cpu: "1"
cpu: 1
}

output {
Expand Down
2 changes: 1 addition & 1 deletion all_of_us/rna_seq/tensorQTL_cis_permutations/tensorqtl_cis_permutations.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ task tensorqtl_cis_permutations {
memory: "~{memory}GB"
disks: "local-disk ~{disk_space} HDD"
bootDiskSizeGb: 25
cpu: "~{num_threads}"
cpu: num_threads
preemptible: "~{num_preempt}"
gpuType: "nvidia-tesla-p100"
gpuCount: "~{num_gpus}"
Expand Down
8 changes: 4 additions & 4 deletions pipelines/wdl/build_indices/BuildIndices.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -362,7 +362,7 @@ task CalculateChromosomeSizes {
docker: "us.gcr.io/broad-gotc-prod/samtools:1.0.0-1.11-1624651616"
preemptible: 3
memory: "3 GiB"
cpu: "1"
cpu: 1
disks: "local-disk 50 HDD"
}
output {
Expand Down Expand Up @@ -536,7 +536,7 @@ task BuildStarSingleNucleus {
memory: "64 GiB"
disks: "local-disk ${disk} HDD"
disk: disk + " GB" # TES
cpu:"16"
cpu: 16
}
}

Expand Down Expand Up @@ -652,7 +652,7 @@ String reference_name = "bwa-mem2-2.2.1-~{organism}-~{genome_source}-build-~{gen
memory: "96GB"
disks: "local-disk 100 HDD"
disk: "100 GB" # TES
cpu: "4"
cpu: 4
}

output {
Expand Down Expand Up @@ -805,7 +805,7 @@ task RecordMetadata {
docker: "ubuntu:20.04"
memory: "5 GiB"
disks: "local-disk 100 HDD"
cpu: "1"
cpu: 1
}
}

Expand Down
2 changes: 1 addition & 1 deletion tasks/wdl/Alignment.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,7 @@ task SamToFastqAndBwaMemAndMba {
docker: "us.gcr.io/broad-gotc-prod/samtools-picard-bwa:1.0.2-0.7.15-2.26.10-1643840748"
preemptible: preemptible_tries
memory: "14 GiB"
cpu: "16"
cpu: 16
disks: "local-disk " + disk_size + " HDD"
}
output {
Expand Down
2 changes: 1 addition & 1 deletion tasks/wdl/BamProcessing.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ task SortSam {
runtime {
docker: docker
disks: "local-disk " + disk_size + " HDD"
cpu: "1"
cpu: 1
memory: "${machine_mem_mb} MiB"
preemptible: preemptible_tries
}
Expand Down
2 changes: 1 addition & 1 deletion tasks/wdl/CopyFilesFromCloudToCloud.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ task CopyFilesFromCloudToCloud {
# We don't have to use an external IP.
runtime {
memory: "2 GiB"
cpu: "1"
cpu: 1
disks: "local-disk 20 HDD"
docker: "us.gcr.io/broad-gotc-prod/dsde-toolbox:stable_04-18-2022"
preemptible: 3
Expand Down
8 changes: 4 additions & 4 deletions tasks/wdl/GermlineVariantDiscovery.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ task HaplotypeCaller_GATK35_GVCF {
docker: docker
preemptible: preemptible_tries
memory: "10000 MiB"
cpu: "1"
cpu: 1
disks: "local-disk " + disk_size + " HDD"
}
output {
Expand Down Expand Up @@ -164,7 +164,7 @@ task HaplotypeCaller_GATK4_VCF {
docker: gatk_docker
preemptible: preemptible_tries
memory: "~{memory_size_mb} MiB"
cpu: "2"
cpu: 2
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
}
Expand Down Expand Up @@ -380,7 +380,7 @@ task CNNScoreVariants {
docker: gatk_docker
preemptible: preemptible_tries
memory: "15000 MiB"
cpu: "2"
cpu: 2
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
}
Expand Down Expand Up @@ -436,7 +436,7 @@ task FilterVariantTranches {

runtime {
memory: "7000 MiB"
cpu: "2"
cpu: 2
bootDiskSizeGb: 15
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
Expand Down
2 changes: 1 addition & 1 deletion tasks/wdl/IlluminaGenotypingArrayTasks.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -538,7 +538,7 @@ task MergePedIntoVcf {
runtime {
docker: "us.gcr.io/broad-gotc-prod/picard-cloud:2.26.11"
memory: "3500 MiB"
cpu: "1"
cpu: 1
disks: "local-disk " + disk_size + " HDD"
preemptible: preemptible_tries
}
Expand Down
Loading