broadinstitute · claymcleod · Apr 11, 2026 · Apr 11, 2026 · Apr 11, 2026 · Apr 11, 2026
diff --git a/all_of_us/PCA/pca_only_no_labels.wdl b/all_of_us/PCA/pca_only_no_labels.wdl
@@ -75,7 +75,7 @@ task ConcatenateChromosomalVcfs {
     runtime {
         docker: bcftools_docker
         memory: "${memory_gb} GB"
-        cpu: "${cpu}"
+        cpu: cpu
         disk: "local-disk ${disk_gb} HDD"
         preemptible: num_preemptible_attempts
     }
@@ -155,7 +155,7 @@ task create_hw_pca_training {
     runtime {
         docker: "hailgenetics/hail:0.2.67"
         memory: "${mem_gb} GB"
-        cpu: "${cpu}"
+        cpu: cpu
         disks: "local-disk ${disk_gb} ${disk_type}" # large SSD is recommended for increased processing speed
     }
 }
@@ -244,7 +244,7 @@ task plot_pca {
     runtime {
         docker: "faizanbashir/python-datascience:3.6"
         memory: "${mem_gb} GB"
-        cpu: "${cpu}"
+        cpu: cpu
         disks: "local-disk ${disk_gb} HDD"
     }
 }
diff --git a/all_of_us/ancestry/determine_hq_sites_intersection.wdl b/all_of_us/ancestry/determine_hq_sites_intersection.wdl
@@ -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"
     }
 }
@@ -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
     }
@@ -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"
     }
 }
@@ -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"
     }
 }
diff --git a/all_of_us/ancestry/run_ancestry.wdl b/all_of_us/ancestry/run_ancestry.wdl
@@ -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"
     }
 }
@@ -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"
     }
 }
@@ -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"
     }
 }
diff --git a/all_of_us/ancestry/run_sample_outlier_qc.wdl b/all_of_us/ancestry/run_sample_outlier_qc.wdl
@@ -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"
     }
 }
@@ -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"
     }
 }

diff --git a/all_of_us/ancestry/run_sample_outlier_qc_plotting.wdl b/all_of_us/ancestry/run_sample_outlier_qc_plotting.wdl
@@ -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"
     }
 }
@@ -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"
     }
 }
@@ -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"
     }
 }
diff --git a/all_of_us/pgx/CyriusStarAlleleCalling.wdl b/all_of_us/pgx/CyriusStarAlleleCalling.wdl
@@ -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 {

diff --git a/all_of_us/pgx/StargazerFromJointVCF.wdl b/all_of_us/pgx/StargazerFromJointVCF.wdl
@@ -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"
     }

diff --git a/all_of_us/rna_seq/AggregateSusieWorkflow.wdl b/all_of_us/rna_seq/AggregateSusieWorkflow.wdl
@@ -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
     }
 
 
@@ -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
     }
 
 

diff --git a/all_of_us/rna_seq/CalculatePhenotypeGroups.wdl b/all_of_us/rna_seq/CalculatePhenotypeGroups.wdl
@@ -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 {

diff --git a/all_of_us/rna_seq/GTEx/aggregate_rsem_results.wdl b/all_of_us/rna_seq/GTEx/aggregate_rsem_results.wdl
@@ -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}"
     }
 

diff --git a/all_of_us/rna_seq/GTEx/markduplicates.wdl b/all_of_us/rna_seq/GTEx/markduplicates.wdl
@@ -1,16 +1,19 @@
-task markduplicates {
+version 1.0
 
-    File input_bam
-    String prefix
-    Int? max_records_in_ram
-    Float? sorting_collection_size_ratio
+task markduplicates {
+    input {
+        File input_bam
+        String prefix
+        Int? max_records_in_ram
+        Float? sorting_collection_size_ratio
+
+        Float memory
+        Int disk_space
+        Int num_threads
+        Int num_preempt
+    }
 
-    Float memory
     Int java_memory = floor(memory - 0.5)
-    Int disk_space
-    Int num_threads
-    Int num_preempt
-
     String output_bam = sub(basename(input_bam), "\\.bam$", ".md.bam")
 
     command {
@@ -32,7 +35,7 @@ task markduplicates {
         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}"
     }
 
@@ -44,4 +47,4 @@ task markduplicates {
 
 workflow markduplicates_workflow {
     call markduplicates
-}
+}
diff --git a/all_of_us/rna_seq/GTEx/remove_IDS_reads.wdl b/all_of_us/rna_seq/GTEx/remove_IDS_reads.wdl
@@ -1,12 +1,15 @@
-task remove_IDS_reads {
-
-    File transcriptome_bam
-    String prefix
+version 1.0
 
-    Int memory
-    Int disk_space
-    Int num_threads
-    Int num_preempt
+task remove_IDS_reads {
+    input {
+        File transcriptome_bam
+        String prefix
+
+        Int memory
+        Int disk_space
+        Int num_threads
+        Int num_preempt
+    }
 
     command {
         set -euo pipefail
@@ -22,7 +25,7 @@ task remove_IDS_reads {
         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}"
     }
 
@@ -34,4 +37,4 @@ task remove_IDS_reads {
 
 workflow rsem_preprocessing_workflow {
     call remove_IDS_reads
-}
+}
diff --git a/all_of_us/rna_seq/GTEx/rnaseq_aou.wdl b/all_of_us/rna_seq/GTEx/rnaseq_aou.wdl
@@ -1,3 +1,5 @@
+version 1.0
+
 # import "https://api.firecloud.org/ga4gh/v1/tools/broad_drc_aou_aux:samToFastq/versions/1/plain-WDL/descriptor" as samtofastq_wdl
 # import "https://api.firecloud.org/ga4gh/v1/tools/gtex_v10_pg:star_align_v10pg/versions/12/plain-WDL/descriptor" as star_align_wdl
 # import "https://api.firecloud.org/ga4gh/v1/tools/gtex_v10_pg:pre_RSEM_processing_v10pg/versions/6/plain-WDL/descriptor" as prersem_wdl
@@ -14,8 +16,10 @@ import "./rnaseqc2.wdl" as rnaseqc_wdl
 
 
 workflow rnaseq_pipeline_bam_workflow {
+    input {
+        String prefix
+    }
 
-    String prefix
     String pipeline_version = "aou_9.0.1"
 
     call samtofastq_wdl.samtofastq {
@@ -39,4 +43,4 @@ workflow rnaseq_pipeline_bam_workflow {
     call rnaseqc_wdl.rnaseqc2 {
         input: bam_file=markduplicates.bam_file, sample_id=prefix
     }
-}
+}
diff --git a/all_of_us/rna_seq/GTEx/rnaseqc2.wdl b/all_of_us/rna_seq/GTEx/rnaseqc2.wdl
@@ -1,18 +1,21 @@
-task rnaseqc2 {
-
-    File bam_file
-    File genes_gtf
-    String sample_id
-    String? strandedness
-    File? intervals_bed
-    File? reference_fasta
-    File? reference_fasta_index
-    String? flags
+version 1.0
 
-    Int memory
-    Int disk_space
-    Int num_threads
-    Int num_preempt
+task rnaseqc2 {
+    input {
+        File bam_file
+        File genes_gtf
+        String sample_id
+        String? strandedness
+        File? intervals_bed
+        File? reference_fasta
+        File? reference_fasta_index
+        String? flags
+
+        Int memory
+        Int disk_space
+        Int num_threads
+        Int num_preempt
+    }
 
     command {
         set -euo pipefail
@@ -38,7 +41,7 @@ task rnaseqc2 {
         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}"
     }
 
@@ -50,4 +53,4 @@ task rnaseqc2 {
 
 workflow rnaseqc2_workflow {
     call rnaseqc2
-}
+}