diff --git a/all_of_us/PCA/pca_only_no_labels.wdl b/all_of_us/PCA/pca_only_no_labels.wdl
index c3808a14c0..1cbe748a35 100644
--- 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"
     }
 }
\ No newline at end of file
diff --git a/all_of_us/ancestry/determine_hq_sites_intersection.wdl b/all_of_us/ancestry/determine_hq_sites_intersection.wdl
index 4fea51e42a..c87fed6b18 100644
--- a/all_of_us/ancestry/determine_hq_sites_intersection.wdl
+++ b/all_of_us/ancestry/determine_hq_sites_intersection.wdl
@@ -51,7 +51,7 @@ workflow determine_hq_sites_intersection {
                 vcf_intervals = training_vcf_so_bgz,
                 vcf_intervals_idx = training_vcf_so_bgz_idx,
                 intersecting_intervals=intersecting_intervals,
-                id = i
+                id = "~{i}"
         }
 
         call intersect_vcfs_as_sites_only {
@@ -92,7 +92,7 @@ workflow determine_hq_sites_intersection {
                 sites_only_vcf_idx = merge_sites_only_intersection.merged_vcf_idx,
                 output_name="full_data_sites_filtered",
                 service_account_json=service_account_json,
-                id = j
+                id = "~{j}"
         }
     }
 
@@ -135,7 +135,7 @@ task sitesOnlyAndHQFilterVcf {
     String output_filename = basename(vcf) + "." + id + ".sites_only.vcf.gz"
     String output_filename_idx = output_filename + ".tbi"
     String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false'
-    String service_account_basename_pre = if (defined(service_account_json)) then service_account_json else ''
+    String service_account_basename_pre = select_first([service_account_json, ''])
     String service_account_basename = basename(service_account_basename_pre)
     String input_vcf_basename = basename(vcf)
     String updated_input_vcf = if (defined(service_account_json)) then input_vcf_basename else vcf
@@ -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
     }
@@ -270,7 +270,7 @@ task filter_by_sites_only {
     String output_filename = basename(output_name) + "." + id + ".vcf.bgz"
     String output_filename_idx = output_filename + ".tbi"
     String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false'
-    String service_account_basename_pre = if (defined(service_account_json)) then service_account_json else ''
+    String service_account_basename_pre = select_first([service_account_json, ''])
     String service_account_basename = basename(service_account_basename_pre)
     String input_vcf_basename = basename(vcf)
     String updated_input_vcf = if (defined(service_account_json)) then input_vcf_basename else vcf
@@ -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"
     }
 }
\ No newline at end of file
diff --git a/all_of_us/ancestry/run_ancestry.wdl b/all_of_us/ancestry/run_ancestry.wdl
index f6379b2efe..b8d948ef8b 100644
--- 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"
     }
 }
\ No newline at end of file
diff --git a/all_of_us/ancestry/run_sample_outlier_qc.wdl b/all_of_us/ancestry/run_sample_outlier_qc.wdl
index fa162b0e83..229c3ffcb9 100644
--- 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
index 9b84c3d00c..e80b8ccc13 100644
--- 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"
     }
 }
\ No newline at end of file
diff --git a/all_of_us/pgx/CyriusStarAlleleCalling.wdl b/all_of_us/pgx/CyriusStarAlleleCalling.wdl
index 53c9a6a63f..45c401725f 100644
--- 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
index a098874684..a964d82666 100644
--- 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
index cd60b5be18..00caac5c00 100644
--- 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
index 4b9c3c11e2..5ed7b00404 100644
--- 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
index 09fd1d6c74..7a1897f5b3 100644
--- 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
index 870d92d11b..425b062f13 100644
--- 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
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/remove_IDS_reads.wdl b/all_of_us/rna_seq/GTEx/remove_IDS_reads.wdl
index 28a3f54b93..4291b174e5 100644
--- 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
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/rnaseq_aou.wdl b/all_of_us/rna_seq/GTEx/rnaseq_aou.wdl
index b4a434a5f8..8d3fd52ec2 100644
--- 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
     }
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/rnaseqc2.wdl b/all_of_us/rna_seq/GTEx/rnaseqc2.wdl
index 68538940d0..ed257b676e 100644
--- 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
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/rsem.wdl b/all_of_us/rna_seq/GTEx/rsem.wdl
index bf09627c6e..b5c3f44a89 100644
--- a/all_of_us/rna_seq/GTEx/rsem.wdl
+++ b/all_of_us/rna_seq/GTEx/rsem.wdl
@@ -1,18 +1,21 @@
-task rsem {
-
-    File transcriptome_bam
-    File rsem_reference
-    String prefix
-
-    Int memory
-    Int disk_space
-    Int num_threads
-    Int num_preempt
+version 1.0
 
-    Int? max_frag_len
-    String? estimate_rspd
-    String? is_stranded
-    String? paired_end
+task rsem {
+    input {
+        File transcriptome_bam
+        File rsem_reference
+        String prefix
+
+        Int memory
+        Int disk_space
+        Int num_threads
+        Int num_preempt
+
+        Int? max_frag_len
+        String? estimate_rspd
+        String? is_stranded
+        String? paired_end
+    }
 
     command {
         set -euo pipefail
@@ -38,7 +41,7 @@ task rsem {
         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 rsem {
 
 workflow rsem_workflow {
     call rsem
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/samtofastq.wdl b/all_of_us/rna_seq/GTEx/samtofastq.wdl
index fa4d74f757..f7f755226b 100644
--- a/all_of_us/rna_seq/GTEx/samtofastq.wdl
+++ b/all_of_us/rna_seq/GTEx/samtofastq.wdl
@@ -1,15 +1,19 @@
-task samtofastq {
+version 1.0
 
-    File input_bam_cram
-    String prefix
-    File? reference_fasta
-    File? reference_fasta_index
+task samtofastq {
+    input {
+        File input_bam_cram
+        String prefix
+        File? reference_fasta
+        File? reference_fasta_index
+
+        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
 
     command {
         set -euo pipefail
@@ -34,7 +38,7 @@ task samtofastq {
         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}"
     }
 
@@ -46,4 +50,4 @@ task samtofastq {
 
 workflow samtofastq_workflow {
     call samtofastq
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/GTEx/star.wdl b/all_of_us/rna_seq/GTEx/star.wdl
index 8368c48197..113380bf78 100644
--- a/all_of_us/rna_seq/GTEx/star.wdl
+++ b/all_of_us/rna_seq/GTEx/star.wdl
@@ -1,46 +1,49 @@
+version 1.0
+
 # This wdl comes from https://github.com/broadinstitute/gtex-pipeline/blob/v10_pg_update/rnaseq/star.wdl
 task star {
+    input {
+        File fastq1
+        File? fastq2
+        String prefix
+        File star_index
 
-    File fastq1
-    File? fastq2
-    String prefix
-    File star_index
-
-    # STAR options
-    Int? outFilterMultimapNmax
-    Int? alignSJoverhangMin
-    Int? alignSJDBoverhangMin
-    Int? outFilterMismatchNmax
-    Float? outFilterMismatchNoverLmax
-    Int? alignIntronMin
-    Int? alignIntronMax
-    Int? alignMatesGapMax
-    String? outFilterType
-    Float? outFilterScoreMinOverLread
-    Float? outFilterMatchNminOverLread
-    Int? limitSjdbInsertNsj
-    String? outSAMstrandField
-    String? outFilterIntronMotifs
-    String? alignSoftClipAtReferenceEnds
-    String? quantMode
-    String? outSAMattrRGline
-    String? outSAMattributes
-    File? varVCFfile
-    String? waspOutputMode
-    Int? chimSegmentMin
-    Int? chimJunctionOverhangMin
-    String? chimOutType
-    Int? chimMainSegmentMultNmax
-    Int? chimOutJunctionFormat
-    File? sjdbFileChrStartEnd
-    String? quantTranscriptomeSAMoutput
-    Int? winAnchorMultimapNmax
-    String? genomeTransformOutput
+        # STAR options
+        Int? outFilterMultimapNmax
+        Int? alignSJoverhangMin
+        Int? alignSJDBoverhangMin
+        Int? outFilterMismatchNmax
+        Float? outFilterMismatchNoverLmax
+        Int? alignIntronMin
+        Int? alignIntronMax
+        Int? alignMatesGapMax
+        String? outFilterType
+        Float? outFilterScoreMinOverLread
+        Float? outFilterMatchNminOverLread
+        Int? limitSjdbInsertNsj
+        String? outSAMstrandField
+        String? outFilterIntronMotifs
+        String? alignSoftClipAtReferenceEnds
+        String? quantMode
+        String? outSAMattrRGline
+        String? outSAMattributes
+        File? varVCFfile
+        String? waspOutputMode
+        Int? chimSegmentMin
+        Int? chimJunctionOverhangMin
+        String? chimOutType
+        Int? chimMainSegmentMultNmax
+        Int? chimOutJunctionFormat
+        File? sjdbFileChrStartEnd
+        String? quantTranscriptomeSAMoutput
+        Int? winAnchorMultimapNmax
+        String? genomeTransformOutput
 
-    Int memory
-    Int disk_space
-    Int num_threads
-    Int num_preempt
+        Int memory
+        Int disk_space
+        Int num_threads
+        Int num_preempt
+    }
 
     command {
         set -euo pipefail
@@ -132,7 +135,7 @@ task star {
         docker: "gcr.io/broad-cga-francois-gtex/gtex_rnaseq@sha256:80c2db3cec3c08630237665e2d2f044f065022e0bbf7a62d0765f51f811818e2"
         memory: "${memory}GB"
         disks: "local-disk ${disk_space} HDD"
-        cpu: "${num_threads}"
+        cpu: num_threads
         preemptible: "${num_preempt}"
     }
 
@@ -144,4 +147,4 @@ task star {
 
 workflow star_workflow {
     call star
-}
\ No newline at end of file
+}
diff --git a/all_of_us/rna_seq/leafcutter_bam_to_junc.wdl b/all_of_us/rna_seq/leafcutter_bam_to_junc.wdl
index 8c3e7be133..058d07c970 100644
--- a/all_of_us/rna_seq/leafcutter_bam_to_junc.wdl
+++ b/all_of_us/rna_seq/leafcutter_bam_to_junc.wdl
@@ -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}"
     }
 
diff --git a/all_of_us/rna_seq/leafcutter_cluster.wdl b/all_of_us/rna_seq/leafcutter_cluster.wdl
index 1ca2fbe0f6..f4d38ffb49 100644
--- a/all_of_us/rna_seq/leafcutter_cluster.wdl
+++ b/all_of_us/rna_seq/leafcutter_cluster.wdl
@@ -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}"
     }
 
diff --git a/all_of_us/rna_seq/prepare_QTL/calculateAF.wdl b/all_of_us/rna_seq/prepare_QTL/calculateAF.wdl
index 786372007d..e7138f15b2 100644
--- a/all_of_us/rna_seq/prepare_QTL/calculateAF.wdl
+++ b/all_of_us/rna_seq/prepare_QTL/calculateAF.wdl
@@ -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
 
         }
 
diff --git a/all_of_us/rna_seq/prepare_QTL/calculateGenotypeDosage.wdl b/all_of_us/rna_seq/prepare_QTL/calculateGenotypeDosage.wdl
index 58b9abd405..48d19f533b 100644
--- a/all_of_us/rna_seq/prepare_QTL/calculateGenotypeDosage.wdl
+++ b/all_of_us/rna_seq/prepare_QTL/calculateGenotypeDosage.wdl
@@ -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"
     }
 
diff --git a/all_of_us/rna_seq/prepare_QTL/calculate_phenotypePCs.wdl b/all_of_us/rna_seq/prepare_QTL/calculate_phenotypePCs.wdl
index 5c36c19bb7..aa26297c41 100644
--- a/all_of_us/rna_seq/prepare_QTL/calculate_phenotypePCs.wdl
+++ b/all_of_us/rna_seq/prepare_QTL/calculate_phenotypePCs.wdl
@@ -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 {
diff --git a/all_of_us/rna_seq/prepare_QTL/prepare_eQTL.wdl b/all_of_us/rna_seq/prepare_QTL/prepare_eQTL.wdl
index 9ad3f388de..00acbbab82 100644
--- a/all_of_us/rna_seq/prepare_QTL/prepare_eQTL.wdl
+++ b/all_of_us/rna_seq/prepare_QTL/prepare_eQTL.wdl
@@ -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 {
diff --git a/all_of_us/rna_seq/prepare_QTL/prepare_sQTL.wdl b/all_of_us/rna_seq/prepare_QTL/prepare_sQTL.wdl
index f733e92103..9eab4bb82b 100644
--- a/all_of_us/rna_seq/prepare_QTL/prepare_sQTL.wdl
+++ b/all_of_us/rna_seq/prepare_QTL/prepare_sQTL.wdl
@@ -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 {
diff --git a/all_of_us/rna_seq/susieR_workflow.wdl b/all_of_us/rna_seq/susieR_workflow.wdl
index 207ecd1de4..9b91bf7166 100644
--- a/all_of_us/rna_seq/susieR_workflow.wdl
+++ b/all_of_us/rna_seq/susieR_workflow.wdl
@@ -73,7 +73,7 @@ task PrepInputs {
         disks: "local-disk 500 SSD"
         preemptible: "${NumPrempt}"
         memory: "2GB"
-        cpu: "1"
+        cpu: 1
     }
     
     output {
@@ -121,7 +121,7 @@ task susieR {
         disks: "local-disk 500 SSD"
         bootDiskSizeGb: 25
         preemptible: "${NumPrempt}"
-        cpu: "1"
+        cpu: 1
     }
 
     output {
diff --git a/all_of_us/rna_seq/tensorQTL_cis_permutations/tensorqtl_cis_permutations.wdl b/all_of_us/rna_seq/tensorQTL_cis_permutations/tensorqtl_cis_permutations.wdl
index 07a05cd19a..447c993c71 100644
--- a/all_of_us/rna_seq/tensorQTL_cis_permutations/tensorqtl_cis_permutations.wdl
+++ b/all_of_us/rna_seq/tensorQTL_cis_permutations/tensorqtl_cis_permutations.wdl
@@ -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}"
diff --git a/pipelines/wdl/build_indices/BuildIndices.wdl b/pipelines/wdl/build_indices/BuildIndices.wdl
index 31ec85d183..149e73d1c8 100644
--- a/pipelines/wdl/build_indices/BuildIndices.wdl
+++ b/pipelines/wdl/build_indices/BuildIndices.wdl
@@ -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 {
@@ -536,7 +536,7 @@ task BuildStarSingleNucleus {
     memory: "64 GiB"
     disks: "local-disk ${disk} HDD"
     disk: disk + " GB" # TES
-    cpu:"16"
+    cpu: 16
   }
 }
 
@@ -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 {
@@ -805,7 +805,7 @@ task RecordMetadata {
     docker: "ubuntu:20.04"
     memory: "5 GiB"
     disks: "local-disk 100 HDD"
-    cpu: "1"
+    cpu: 1
   }
 }
 
diff --git a/pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl b/pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl
index b11f66d70b..548ae502cf 100644
--- a/pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl
+++ b/pipelines/wdl/glimpse/low_pass_imputation/Glimpse2LowPassImputation.wdl
@@ -288,7 +288,7 @@ task ComputeShardsAndMemoryPerShard {
 
     output {
         Array[String] reference_chunk_file_paths = read_lines("reference_shard_file_paths.tsv")
-        Array[Int] mem_gb_per_chunk = read_lines("memory_per_chunk.tsv")
+        Array[String] mem_gb_per_chunk = read_lines("memory_per_chunk.tsv")
     }
 }
 
diff --git a/tasks/wdl/Alignment.wdl b/tasks/wdl/Alignment.wdl
index f3c150bbfc..0e35c01e11 100644
--- a/tasks/wdl/Alignment.wdl
+++ b/tasks/wdl/Alignment.wdl
@@ -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 {
diff --git a/tasks/wdl/BamProcessing.wdl b/tasks/wdl/BamProcessing.wdl
index cf4ff4d4e2..2f99d60969 100644
--- a/tasks/wdl/BamProcessing.wdl
+++ b/tasks/wdl/BamProcessing.wdl
@@ -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
   }
diff --git a/tasks/wdl/CopyFilesFromCloudToCloud.wdl b/tasks/wdl/CopyFilesFromCloudToCloud.wdl
index aa52c83716..b98806e4db 100644
--- a/tasks/wdl/CopyFilesFromCloudToCloud.wdl
+++ b/tasks/wdl/CopyFilesFromCloudToCloud.wdl
@@ -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
diff --git a/tasks/wdl/Funcotator.wdl b/tasks/wdl/Funcotator.wdl
index 73b8621d13..12e0f9bcb6 100644
--- a/tasks/wdl/Funcotator.wdl
+++ b/tasks/wdl/Funcotator.wdl
@@ -160,9 +160,9 @@ task Funcotate {
       -O ~{output_vcf} \
       ~{true="-L" false="" defined(interval_list)} ~{default="" interval_list} \
       ~{true="--transcript-selection-mode" false="" defined(transcript_selection_mode)} ~{default="" transcript_selection_mode} \
-      ~{true="--transcript-list" false="" defined(transcript_selection_list)} ~{default="" sep=" --transcript-list " transcript_selection_list} \
-      ~{true="--annotation-default" false="" defined(annotation_defaults)} ~{default="" sep=" --annotation-default " annotation_defaults} \
-      ~{true="--annotation-override" false="" defined(annotation_overrides)} ~{default="" sep=" --annotation-override " annotation_overrides} \
+      ~{sep=" " prefix("--transcript-list ", select_first([transcript_selection_list, []]))} \
+      ~{sep=" " prefix("--annotation-default ", select_first([annotation_defaults, []]))} \
+      ~{sep=" " prefix("--annotation-override ", select_first([annotation_overrides, []]))} \
       ~{true="--remove-filtered-variants" false="" filter_funcotations} \
       ~{default="" extra_args}
   >>>
diff --git a/tasks/wdl/GermlineVariantDiscovery.wdl b/tasks/wdl/GermlineVariantDiscovery.wdl
index 4ab5964cdb..c70dcf980f 100644
--- a/tasks/wdl/GermlineVariantDiscovery.wdl
+++ b/tasks/wdl/GermlineVariantDiscovery.wdl
@@ -64,7 +64,7 @@ task HaplotypeCaller_GATK35_GVCF {
       --max_alternate_alleles 3 \
       -variant_index_parameter 128000 \
       -variant_index_type LINEAR \
-      -contamination ~{default=0 contamination} \
+      -contamination ~{default="0" contamination} \
       --read_filter OverclippedRead
 
   }
@@ -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 {
@@ -147,7 +147,7 @@ task HaplotypeCaller_GATK4_VCF {
       -I ~{input_bam} \
       -L ~{interval_list} \
       -O ~{output_file_name} \
-      -contamination ~{default=0 contamination} \
+      -contamination ~{default="0" contamination} \
       -G StandardAnnotation -G StandardHCAnnotation ~{true="-G AS_StandardAnnotation" false="" make_gvcf} \
       ~{true="--dragen-mode" false="" run_dragen_mode_variant_calling} \
       ~{false="--disable-spanning-event-genotyping" true="" use_spanning_event_genotyping} \
@@ -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"
   }
@@ -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"
   }
@@ -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
diff --git a/tasks/wdl/IlluminaGenotypingArrayTasks.wdl b/tasks/wdl/IlluminaGenotypingArrayTasks.wdl
index ab362104a9..eb1f2e9261 100644
--- a/tasks/wdl/IlluminaGenotypingArrayTasks.wdl
+++ b/tasks/wdl/IlluminaGenotypingArrayTasks.wdl
@@ -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
   }
diff --git a/tasks/wdl/JointGenotypingTasks.wdl b/tasks/wdl/JointGenotypingTasks.wdl
index 9e6378a9b5..c73f403b20 100644
--- a/tasks/wdl/JointGenotypingTasks.wdl
+++ b/tasks/wdl/JointGenotypingTasks.wdl
@@ -301,7 +301,7 @@ task HardFilterAndMakeSitesOnlyVcf {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "1"
+    cpu: 1
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -363,7 +363,7 @@ task IndelsVariantRecalibrator {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "2"
+    cpu: 2
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -431,7 +431,7 @@ task SNPsVariantRecalibratorCreateModel {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "2"
+    cpu: 2
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -578,7 +578,7 @@ task GatherTranches {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "2"
+    cpu: 2
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -638,7 +638,7 @@ task ApplyRecalibration {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "1"
+    cpu: 1
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -685,7 +685,7 @@ task GatherVcfs {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "1"
+    cpu: 1
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -856,7 +856,7 @@ task GatherVariantCallingMetrics {
 
   runtime {
     memory: "~{machine_mem_mb} MiB"
-    cpu: "1"
+    cpu: 1
     bootDiskSizeGb: 15
     disks: "local-disk " + disk_size_gb + " HDD"
     preemptible: 1
@@ -897,7 +897,7 @@ task CrossCheckFingerprint {
   Int cpu = if num_gvcfs < 32 then num_gvcfs else 32
   # Compute memory to use based on the CPU count, following the pattern of
   # 3.75GiB / cpu used by GCP's pricing: https://cloud.google.com/compute/pricing
-  Int memory = if defined(machine_mem_mb) then machine_mem_mb else round(cpu * 3.75 * 1024)
+  Int memory = select_first([machine_mem_mb, round(cpu * 3.75 * 1024)])
   Int java_mem = memory - 512
 
   String output_name = output_base_name + ".fingerprintcheck"
@@ -1057,10 +1057,18 @@ task GetFingerprintingIntervalIndices {
     else
       touch indices.out
     fi
+
+    python3 -c "
+with open('indices.out') as f:
+    indices = [int(line.strip()) for line in f if line.strip()]
+import json
+with open('indices.json', 'w') as out:
+    json.dump(indices, out)
+"
   >>>
 
   output {
-    Array[String] indices_to_fingerprint = read_lines("indices.out")
+    Array[Int] indices_to_fingerprint = read_json("indices.json")
     File all_sorted_interval_list = "all.sorted.interval_list"
     File all_interval_list = "all.interval_list"
     File hdb_interval_list = "hdb.interval_list"
diff --git a/tasks/wdl/Qc.wdl b/tasks/wdl/Qc.wdl
index 36e4708dfb..3d2492e34d 100644
--- a/tasks/wdl/Qc.wdl
+++ b/tasks/wdl/Qc.wdl
@@ -431,9 +431,9 @@ task ValidateSamFile {
       OUTPUT=~{report_filename} \
       REFERENCE_SEQUENCE=~{ref_fasta} \
       ~{"MAX_OUTPUT=" + max_output} \
-      IGNORE=~{default="null" sep=" IGNORE=" ignore} \
+      ~{sep=" " prefix("IGNORE=", select_first([ignore, ["null"]]))} \
       MODE=VERBOSE \
-      ~{default='SKIP_MATE_VALIDATION=false' true='SKIP_MATE_VALIDATION=true' false='SKIP_MATE_VALIDATION=false' is_outlier_data} \
+      ~{true='SKIP_MATE_VALIDATION=true' false='SKIP_MATE_VALIDATION=false' select_first([is_outlier_data, false])} \
       IS_BISULFITE_SEQUENCED=false
   }
   runtime {
@@ -503,7 +503,7 @@ task CollectRawWgsMetrics {
   Int disk_size = ceil(size(input_bam, "GiB") + ref_size) + additional_disk
 
   Int memory_size = ceil((if (disk_size < 110) then 5 else 7) * memory_multiplier)
-  String java_memory_size = (memory_size - 1) * 1000
+  Int java_memory_size = (memory_size - 1) * 1000
 
   command {
     java -Xms~{java_memory_size}m -jar /usr/picard/picard.jar \
diff --git a/tasks/wdl/StarAlign.wdl b/tasks/wdl/StarAlign.wdl
index 3a1454d509..77a1e721da 100644
--- a/tasks/wdl/StarAlign.wdl
+++ b/tasks/wdl/StarAlign.wdl
@@ -876,6 +876,6 @@ task STARGenomeRefVersion {
     memory: "2 GiB"
     disks: "local-disk ${disk} HDD"
     disk: disk + " GB" # TES
-    cpu:"1"
+    cpu: 1
   }
 }
\ No newline at end of file
diff --git a/tasks/wdl/TerraCopyFilesFromCloudToCloud.wdl b/tasks/wdl/TerraCopyFilesFromCloudToCloud.wdl
index 1860151bff..9c86095249 100644
--- a/tasks/wdl/TerraCopyFilesFromCloudToCloud.wdl
+++ b/tasks/wdl/TerraCopyFilesFromCloudToCloud.wdl
@@ -41,7 +41,7 @@ task TerraCopyFilesFromCloudToCloud {
 
   runtime {
     memory: "16 GiB"
-    cpu: "1"
+    cpu: 1
     disks: "local-disk 32 HDD"
     docker: "gcr.io/google.com/cloudsdktool/google-cloud-cli:499.0.0-slim"
     preemptible: 3
diff --git a/tasks/wdl/UltimaGenomicsWholeGenomeGermlineTasks.wdl b/tasks/wdl/UltimaGenomicsWholeGenomeGermlineTasks.wdl
index d0e5ca85fc..3a3072e596 100644
--- a/tasks/wdl/UltimaGenomicsWholeGenomeGermlineTasks.wdl
+++ b/tasks/wdl/UltimaGenomicsWholeGenomeGermlineTasks.wdl
@@ -811,7 +811,7 @@ task CollectWgsMetrics {
     USE_FAST_ALGORITHM=false \
     COUNT_UNPAIRED=true \
     COVERAGE_CAP=12500 \
-    READ_LENGTH=~{default=250 read_length}
+    READ_LENGTH=~{default="250" read_length}
   }
 
   runtime {
@@ -863,7 +863,7 @@ task CollectRawWgsMetrics {
     OUTPUT=~{metrics_filename} \
     COUNT_UNPAIRED=true \
     USE_FAST_ALGORITHM=false \
-    READ_LENGTH=~{default=250 read_length}
+    READ_LENGTH=~{default="250" read_length}
   }
 
   runtime {
diff --git a/tasks/wdl/Utilities.wdl b/tasks/wdl/Utilities.wdl
index e6a1aeec17..63bb6e7342 100644
--- a/tasks/wdl/Utilities.wdl
+++ b/tasks/wdl/Utilities.wdl
@@ -149,7 +149,7 @@ task ConvertToCram {
     docker: "us.gcr.io/broad-gotc-prod/samtools:1.0.0-1.11-1624651616"
     preemptible: preemptible_tries
     memory: "3 GiB"
-    cpu: "1"
+    cpu: 1
     disks: "local-disk " + disk_size + " HDD"
   }
   output {
@@ -180,7 +180,7 @@ task ConvertToBam {
     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 200 HDD"
   }
   output {
diff --git a/tasks/wdl/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl b/tasks/wdl/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl
index 81df8d68dd..790028eab1 100644
--- a/tasks/wdl/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl
+++ b/tasks/wdl/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl
@@ -45,7 +45,7 @@ task BuildBWAreference {
 	 memory: "96GB"
 	 disks: "local-disk 100 HDD"
      disk: "100 GB" # TES
-	 cpu: "4"
+	 cpu: 4
      }
 
      output {
diff --git a/verification/VerifyMetrics.wdl b/verification/VerifyMetrics.wdl
index 3baa400998..b0cc4ee9d9 100644
--- a/verification/VerifyMetrics.wdl
+++ b/verification/VerifyMetrics.wdl
@@ -84,7 +84,7 @@ task CompareMetricFiles {
       --INPUT ~{file1} \
       --INPUT ~{file2} \
       --OUTPUT ~{output_file} \
-      ~{true="--METRICS_TO_IGNORE" false="" length(metrics_to_ignore) > 0} ~{default="" sep=" --METRICS_TO_IGNORE " metrics_to_ignore} \
+      ~{sep=" " prefix("--METRICS_TO_IGNORE ", metrics_to_ignore)} \
       ~{sep=" " extra_args}
   >>>
 
diff --git a/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl b/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl
index c0a3cfaedd..3956de1619 100644
--- a/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl
+++ b/verification/VerifyUltimaGenomicsWholeGenomeCramOnly.wdl
@@ -99,7 +99,7 @@ task CompareOldMetricFiles {
     --INPUT ~{file1} \
     --INPUT ~{file2} \
     --OUTPUT ~{output_file} \
-    ~{true="--METRICS_TO_IGNORE" false="" length(metrics_to_ignore) > 0} ~{default="" sep=" --METRICS_TO_IGNORE " metrics_to_ignore}
+    ~{sep=" " prefix("--METRICS_TO_IGNORE ", metrics_to_ignore)}
   >>>
 
   runtime {
diff --git a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
index ec2f2bcbea..95aa575c54 100755
--- a/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
+++ b/verification/VerifyUltimaGenomicsWholeGenomeGermline.wdl
@@ -184,7 +184,7 @@ task CompareOldMetricFiles {
     --INPUT ~{file1} \
     --INPUT ~{file2} \
     --OUTPUT ~{output_file} \
-    ~{true="--METRICS_TO_IGNORE" false="" length(metrics_to_ignore) > 0} ~{default="" sep=" --METRICS_TO_IGNORE " metrics_to_ignore}
+    ~{sep=" " prefix("--METRICS_TO_IGNORE ", metrics_to_ignore)}
   >>>
 
   runtime {
diff --git a/verification/test-wdls/TestArrayImputationQC.wdl b/verification/test-wdls/TestArrayImputationQC.wdl
index 4bc162b93f..064c6c74da 100644
--- a/verification/test-wdls/TestArrayImputationQC.wdl
+++ b/verification/test-wdls/TestArrayImputationQC.wdl
@@ -49,7 +49,7 @@ workflow TestArrayImputationQC {
     call WriteMapToTsv {
       input:
         input_map = {
-          "passes_qc": InputQC.passes_qc,
+          "passes_qc": "~{InputQC.passes_qc}",
           "qc_messages": InputQC.qc_messages
         }
     }