wustl-oncology · Layth17 · Dec 1, 2022 · Oct 29, 2022 · Oct 29, 2022 · Oct 29, 2022
diff --git a/definitions/tools/add_strelka_gt.wdl b/definitions/tools/add_strelka_gt.wdl
@@ -7,6 +7,8 @@ task addStrelkaGt {
 
   Int space_needed_gb = 10 + round(size(vcf, "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "ubuntu:bionic"
     memory: "4GB"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/add_string_at_line.wdl b/definitions/tools/add_string_at_line.wdl
@@ -10,6 +10,8 @@ task addStringAtLine {
 
   Int space_needed_gb = 10 + round(2*size(input_file, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "ubuntu:xenial"
     memory: "4GB"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/add_string_at_line_bgzipped.wdl b/definitions/tools/add_string_at_line_bgzipped.wdl
@@ -10,6 +10,8 @@ task addStringAtLineBgzipped {
 
   Int space_needed_gb = 10 + round(2*size(input_file, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "quay.io/biocontainers/samtools:1.11-h6270b1f_0"
     memory: "4GB"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/add_vep_fields_to_table.wdl b/definitions/tools/add_vep_fields_to_table.wdl
@@ -10,6 +10,8 @@ task addVepFieldsToTable {
 
   Int space_needed_gb = 10 + round(size([vcf, tsv], "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "griffithlab/vatools:4.1.0"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/agfusion.wdl b/definitions/tools/agfusion.wdl
@@ -9,6 +9,8 @@ task agfusion {
   }
 
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/agfusion:1.3.1-ensembl-105"
     memory: "32GB"
     cpu: 4

diff --git a/definitions/tools/annotsv.wdl b/definitions/tools/annotsv.wdl
@@ -10,6 +10,8 @@ task annotsv {
 
   Int space_needed_gb = 10 + round(size(snps_vcf, "GB") + size(input_vcf, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "8GB"
     docker: "mgibio/annotsv-cwl:2.1"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/annotsv_filter.wdl b/definitions/tools/annotsv_filter.wdl
@@ -11,6 +11,8 @@ task annotsvFilter {
 
   Int space_needed_gb = 10 + round(2*size(annotsv_tsv, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "python:3"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/bam_readcount.wdl b/definitions/tools/bam_readcount.wdl
@@ -16,6 +16,8 @@ task bamReadcount {
 
   Int space_needed_gb = 10 + round(size([bam, bam_bai, reference, reference_fai, reference_dict, vcf], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/bam_readcount_helper-cwl:1.1.1"
     memory: "16GB"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/bam_to_bigwig.wdl b/definitions/tools/bam_to_bigwig.wdl
@@ -13,6 +13,8 @@ task bamToBigwig {
   Float reference_size_gb = size([reference, reference_fai, reference_dict], "GB")
   Int space_needed_gb = 10 + round(3*bam_size_gb + reference_size_gb)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "32GB"
     docker: "quay.io/biocontainers/cgpbigwig:1.4.0--h93d22ca_0"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/bam_to_cram.wdl b/definitions/tools/bam_to_cram.wdl
@@ -15,6 +15,8 @@ task bamToCram {
   Float reference_size = size([reference, reference_fai, reference_dict], "GB")
   Int size_needed_gb = 10 + round(size(bam, "GB") * 2 + reference_size)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
     memory: "4GB"
     disks: "local-disk ~{size_needed_gb} HDD"

diff --git a/definitions/tools/bam_to_fastq.wdl b/definitions/tools/bam_to_fastq.wdl
@@ -6,6 +6,8 @@ task bamToFastq {
   # ran into issue at 3*, bump to 10*
   Int space_needed_gb = 10 + round(10*size(bam, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/rnaseq:1.0.0"
     cpu: 1
     memory: "6GB"

diff --git a/definitions/tools/bcftools_merge.wdl b/definitions/tools/bcftools_merge.wdl
@@ -12,6 +12,8 @@ task bcftoolsMerge {
 
   Int space_needed_gb = 10 + round(2 * size(vcfs, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "mgibio/bcftools-cwl:1.12"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/bedgraph_to_bigwig.wdl b/definitions/tools/bedgraph_to_bigwig.wdl
@@ -8,6 +8,8 @@ task bedgraphToBigwig {
 
   Int space_needed_gb = 10 + round(size(methylation_bedgraph, "GB") + size(reference_sizes, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/bisulfite:v1.4"
     memory: "32GB"
     cpu: 1

diff --git a/definitions/tools/bgzip.wdl b/definitions/tools/bgzip.wdl
@@ -7,6 +7,8 @@ task bgzip {
 
   Int space_needed_gb = 10 + round(size(file, "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/biscuit_align.wdl b/definitions/tools/biscuit_align.wdl
@@ -11,6 +11,8 @@ task biscuitAlign {
   Int cores = 12
   Int space_needed_gb = 10 + round(2*size([reference_index, fastq1, fastq2], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "32GB"
     cpu: cores
     docker: "mgibio/biscuit:0.3.8"

diff --git a/definitions/tools/biscuit_markdup.wdl b/definitions/tools/biscuit_markdup.wdl
@@ -9,6 +9,8 @@ task biscuitMarkdup {
   Int cores = 4
   Int space_needed_gb = 10 + round(2*size(bam, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     cpu: cores
     memory: "24GB"
     docker: "mgibio/biscuit:0.3.8"

diff --git a/definitions/tools/biscuit_pileup.wdl b/definitions/tools/biscuit_pileup.wdl
@@ -10,6 +10,8 @@ task biscuitPileup {
 
   Int space_needed_gb = 10 + round(2*size([bam, reference], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "48GB"
     cpu: cores
     docker: "mgibio/biscuit:0.3.8"

diff --git a/definitions/tools/bisulfite_qc.wdl b/definitions/tools/bisulfite_qc.wdl
@@ -11,6 +11,8 @@ task bisulfiteQc {
 
   Int space_needed_gb = 10 + round(size([vcf, bam, reference, reference_fai, QCannotation], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     cpu: 1
     memory: "16GB"
     bootDiskSizeGb: 20

diff --git a/definitions/tools/bisulfite_vcf2bed.wdl b/definitions/tools/bisulfite_vcf2bed.wdl
@@ -10,6 +10,8 @@ task bisulfiteVcf2bed {
 
   Int space_needed_gb = 10 + round(size([vcf, reference], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/biscuit:0.3.8"
     memory: "16GB"
     cpu: 2

diff --git a/definitions/tools/bqsr.wdl b/definitions/tools/bqsr.wdl
@@ -130,6 +130,7 @@ task CreateSequenceGroupingTSV {
     CODE
   >>>
   runtime {
+    maxRetries: 2
     preemptible: preemptible_tries
     docker: "python:2.7"
     memory: "2 GiB"
@@ -158,6 +159,7 @@ task bqsr {
   Float reference_size = size([reference, reference_fai, reference_dict], "GB")
   Int space_needed_gb = 10 + round(known_sites_size  + bam_size + reference_size)
   runtime {
+    maxRetries: 2
     docker: "broadinstitute/gatk:4.1.8.1"
     memory: "6GB"
     disks: "local-disk ~{space_needed_gb} SSD"
@@ -192,6 +194,7 @@ task GatherBqsrReports {
       -O bqsr_report.txt
   }
   runtime {
+    maxRetries: 2
     preemptible: preemptible_tries
     docker: "broadinstitute/gatk:4.1.8.1"
     memory: "4 GiB"
@@ -218,6 +221,8 @@ task applyBqsr {
 
   Int space_needed_gb = 10 + round(size([bqsr_table, reference, reference_fai, reference_dict], "GB") + size([bam, bam_bai], "GB") * 2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "broadinstitute/gatk:4.1.8.1"
     memory: "18GB"
     disks: "local-disk ~{space_needed_gb} SSD"
@@ -251,6 +256,7 @@ task GatherBamFiles {
   Int command_mem_gb = ceil(mem_size_gb) - 1
   Int space_needed_gb = 10 + round(bam_size * 2.5)
   runtime {
+    maxRetries: 2
     preemptible: preemptible_tries
     docker: "broadinstitute/gatk:4.1.8.1"
     memory: "3 GiB"

diff --git a/definitions/tools/cat_all.wdl b/definitions/tools/cat_all.wdl
@@ -7,6 +7,8 @@ task catAll {
 
   Int space_needed_gb = 10 + round(size(region_pindel_outs, "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "ubuntu:xenial"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/cat_out.wdl b/definitions/tools/cat_out.wdl
@@ -7,6 +7,8 @@ task catOut {
 
   Int space_needed_gb = 10 + round(size(pindel_outs, "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     docker: "ubuntu:xenial"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/cnvkit_batch.wdl b/definitions/tools/cnvkit_batch.wdl
@@ -21,6 +21,8 @@ task cnvkitBatch {
 
   Int size_needed_gb = 10 + round(size([tumor_bam, bait_intervals, access, normal_bam, reference_fasta, reference_cnn], "GB") * 2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "4GB"
     cpu: 1
     # We use a forked cnvkit so we can get access to root privileges

diff --git a/definitions/tools/cnvkit_vcf_export.wdl b/definitions/tools/cnvkit_vcf_export.wdl
@@ -11,6 +11,8 @@ task cnvkitVcfExport {
 
   Int space_needed_gb = 10 + round(2*size([cns_file, cnr_file], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "8GB"
     docker: "mgibio/cnvkit:0.9.9"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/cnvnator.wdl b/definitions/tools/cnvnator.wdl
@@ -11,6 +11,8 @@ task cnvnator {
   }
 
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/cnvnator-cwl:0.4"
     memory: "20GB"
     bootDiskSizeGb: 10

diff --git a/definitions/tools/collect_alignment_summary_metrics.wdl b/definitions/tools/collect_alignment_summary_metrics.wdl
@@ -11,7 +11,9 @@ task collectAlignmentSummaryMetrics {
   }
 
   Int space_needed_gb = 10 + round(size([bam, bam_bai, reference, reference_fai, reference_dict],"GB"))
-  runtime{
+  runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "48GB"
     docker: "broadinstitute/picard:2.23.6"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/collect_gc_bias_metrics.wdl b/definitions/tools/collect_gc_bias_metrics.wdl
@@ -16,6 +16,8 @@ task collectGcBiasMetrics {
   Float reference_size_gb = size([reference, reference_fai, reference_dict], "GB")
   Int space_needed_gb = 10 + round(bam_size_gb + reference_size_gb)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "48GB"
     docker: "broadinstitute/picard:2.23.6"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/collect_hs_metrics.wdl b/definitions/tools/collect_hs_metrics.wdl
@@ -20,7 +20,9 @@ task collectHsMetrics {
   }
 
   Int space_needed_gb = 10 + round(size([bam, bam_bai, reference, reference_fai, reference_dict, bait_intervals, target_intervals], "GB"))
-  runtime{
+  runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "60GB"
     docker: "broadinstitute/picard:2.23.6"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/collect_insert_size_metrics.wdl b/definitions/tools/collect_insert_size_metrics.wdl
@@ -12,6 +12,8 @@ task collectInsertSizeMetrics {
 
   Int space_needed_gb = 10 + round(size([bam, bam_bai, reference, reference_fai, reference_dict], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "broadinstitute/picard:2.23.6"
     memory: "48GB"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/collect_wgs_metrics.wdl b/definitions/tools/collect_wgs_metrics.wdl
@@ -18,6 +18,8 @@ task collectWgsMetrics {
   Float intervals_size = size(intervals, "GB")
   Int space_needed_gb = 10 + round(bam_size + reference_size + intervals_size)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "48GB"
     docker: "broadinstitute/picard:2.23.6"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/combine_variants.wdl b/definitions/tools/combine_variants.wdl
@@ -19,6 +19,8 @@ task combineVariants {
   Float strelka_size = size([strelka_vcf, strelka_vcf_tbi], "GB")
   Int space_needed_gb = 10 + round(ref_size + mutect_size + varscan_size + strelka_size)*2
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "9GB"
     docker:  "mgibio/gatk-cwl:3.6.0"
     bootDiskSizeGb: 25

diff --git a/definitions/tools/combine_variants_wgs.wdl b/definitions/tools/combine_variants_wgs.wdl
@@ -19,6 +19,8 @@ task combineVariantsWgs {
   Float strelka_size = size([strelka_vcf, strelka_vcf_tbi], "GB")
   Int space_needed_gb = 10 + round(ref_size + mutect_size + varscan_size + strelka_size)*2
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "9GB"
     docker:  "mgibio/gatk-cwl:3.6.0"
     bootDiskSizeGb: 25

diff --git a/definitions/tools/concordance.wdl b/definitions/tools/concordance.wdl
@@ -18,6 +18,8 @@ task concordance {
 
   Int space_needed_gb = 10 + round(size([vcf, reference, reference_fai, reference_dict, bam_1, bam_1_bai, bam_2, bam_2_bai, bam_3, bam_3_bai], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     cpu: 1
     memory: "8GB"
     bootDiskSizeGb: 10

diff --git a/definitions/tools/docm_add_variants.wdl b/definitions/tools/docm_add_variants.wdl
@@ -15,6 +15,8 @@ task docmAddVariants {
   Float docm_size = size([docm_vcf, docm_vcf_tbi], "GB")
   Int space_needed_gb = 10 + round(reference_size + callers_size + docm_size)*2
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "9GB"
     bootDiskSizeGb: 25
     docker: "mgibio/gatk-cwl:3.6.0"

diff --git a/definitions/tools/docm_gatk_haplotype_caller.wdl b/definitions/tools/docm_gatk_haplotype_caller.wdl
@@ -24,6 +24,8 @@ task docmGatkHaplotypeCaller {
   Float copied_size = size([docm_vcf, interval_list], "GB")
   Int space_needed_gb = 10 + round(copied_size*3 + size([reference, reference_fai, reference_dict, normal_bam, normal_bam_bai, bam, bam_bai, docm_vcf_tbi], "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "9GB"
     docker: "broadinstitute/gatk:4.1.2.0"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/downsample.wdl b/definitions/tools/downsample.wdl
@@ -18,6 +18,8 @@ task downsample {
   Float reference_size = size([reference, reference_fai, reference_dict], "GB")
   Int space_needed_gb = 10 + round(reference_size + size(sam, "GB") * 2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "18GB"
     docker: "broadinstitute/gatk:4.1.4.1"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/duphold.wdl b/definitions/tools/duphold.wdl
@@ -14,6 +14,8 @@ task duphold {
   Int cores = 2
   Int space_needed_gb = 10
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "10GB"
     docker: "mgibio/duphold-cwl:0.1.5"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/echo_file.wdl b/definitions/tools/echo_file.wdl
@@ -4,6 +4,8 @@ task echoFile {
   input {}
 
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "ubuntu:bionic"
   }
 

diff --git a/definitions/tools/extract_hla_alleles.wdl b/definitions/tools/extract_hla_alleles.wdl
@@ -8,6 +8,8 @@ task extractHlaAlleles {
 
   Int space_needed_gb = 10 + round(size(file, "GB"))
   runtime {
+    preemptible: 1
+    maxRetries: 2
     memory: "2GB"
     docker: "ubuntu:xenial"
     disks: "local-disk ~{space_needed_gb} HDD"

diff --git a/definitions/tools/filter_known_variants.wdl b/definitions/tools/filter_known_variants.wdl
@@ -10,6 +10,8 @@ task filterKnownVariants {
 
   Int space_needed_gb = 10 + round(size([vcf, vcf_tbi, validated_variants, validated_variants_tbi], "GB")*2)
   runtime {
+    preemptible: 1
+    maxRetries: 2
     docker: "mgibio/bcftools-cwl:1.12"
     memory: "8GB"
     disks:  "local-disk ~{space_needed_gb} HDD"