diff --git a/definitions/tools/add_strelka_gt.wdl b/definitions/tools/add_strelka_gt.wdl index 9da2ce7a..2e4d3d70 100644 --- 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 index 4da42551..f656922f 100644 --- 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 index cbcf60b2..e0630ef3 100644 --- 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 index a12b2398..708a0551 100644 --- 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 index 92ebcb53..dff2cc82 100644 --- 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 index 4bafa61d..2c6356fe 100644 --- 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 index 93a7c5d8..288dc1ab 100644 --- 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 index d3a8bcb3..9cf761fd 100644 --- 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 index df5865cb..852c4e63 100644 --- 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 index cc60d11b..3ce11e18 100644 --- 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 index 5a879bea..42774b99 100644 --- 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 index c00b3898..9c4965ae 100644 --- 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 index 9e381f87..a13bcbbb 100644 --- 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 index 20c0c587..3efea077 100644 --- 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 index 2c1e8574..ec47d78f 100644 --- 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 index b1b975d1..2e8ea5a7 100644 --- 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 index 4f3e378d..a2b00fa0 100644 --- 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 index 6c9d242e..6eae8075 100644 --- 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 index 739d447a..4f02a1a2 100644 --- 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 index c9c80cc6..063051fb 100644 --- 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 index 33da9dbb..64d0828d 100644 --- 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 index cd1a13ed..24f9936e 100644 --- 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 index 182d4545..c300c9d2 100644 --- 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 index 3c42185c..9ad9b489 100644 --- 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 index 716358cb..18609ed3 100644 --- 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 index 6df674a6..896c1604 100644 --- 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 index 93130550..b843e881 100644 --- 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 index 44d04411..64959491 100644 --- 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 index aa9df3a6..b4196648 100644 --- 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 index fe7830d9..a6f6f091 100644 --- 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 index 8b7eb56a..939b445d 100644 --- 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 index d87f5467..258c8378 100644 --- 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 index d4043619..55fba7f0 100644 --- 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 index c398f4f3..2d342c61 100644 --- 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 index 6422f8e2..16d9e0d2 100644 --- 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 index 98283ee7..13576e72 100644 --- 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 index 6725acfa..1e4466c8 100644 --- 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 index c1534b74..876b8801 100644 --- 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 index c4e8f67b..736b1781 100644 --- 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 index 4027d3e6..e0fdfe6a 100644 --- 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" diff --git a/definitions/tools/filter_sv_vcf_blocklist_bedpe.wdl b/definitions/tools/filter_sv_vcf_blocklist_bedpe.wdl index 297faa9a..54452362 100644 --- a/definitions/tools/filter_sv_vcf_blocklist_bedpe.wdl +++ b/definitions/tools/filter_sv_vcf_blocklist_bedpe.wdl @@ -10,6 +10,8 @@ task filterSvVcfBlocklistBedpe { Int space_needed_gb = 10 runtime { + preemptible: 1 + maxRetries: 2 memory: "8GB" docker: "mgibio/basespace_chromoseq:v12" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_sv_vcf_depth.wdl b/definitions/tools/filter_sv_vcf_depth.wdl index 3cbcf07b..3acc7125 100644 --- a/definitions/tools/filter_sv_vcf_depth.wdl +++ b/definitions/tools/filter_sv_vcf_depth.wdl @@ -11,6 +11,8 @@ task filterSvVcfDepth { Int space_needed_gb = 10 + round(2*size(input_vcf, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "mgibiobcftools-cwl:1.12" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_sv_vcf_read_support.wdl b/definitions/tools/filter_sv_vcf_read_support.wdl index 8969bde1..4636f534 100644 --- a/definitions/tools/filter_sv_vcf_read_support.wdl +++ b/definitions/tools/filter_sv_vcf_read_support.wdl @@ -12,6 +12,8 @@ task filterSvVcfReadSupport { Int space_needed_gb = 10 runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "bcftools-cwl:1.12" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_sv_vcf_size.wdl b/definitions/tools/filter_sv_vcf_size.wdl index 8a34c4b5..587eaab6 100644 --- a/definitions/tools/filter_sv_vcf_size.wdl +++ b/definitions/tools/filter_sv_vcf_size.wdl @@ -10,6 +10,8 @@ task filterSvVcfSize { Int space_needed_gb = 10 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/filter_vcf_cle.wdl b/definitions/tools/filter_vcf_cle.wdl index b215c252..ddb91494 100644 --- a/definitions/tools/filter_vcf_cle.wdl +++ b/definitions/tools/filter_vcf_cle.wdl @@ -8,6 +8,8 @@ task filterVcfCle { Int space_needed_gb = 10 + round(size(vcf, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/cle:v1.3.1" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_vcf_coding_variant.wdl b/definitions/tools/filter_vcf_coding_variant.wdl index b624d851..00b9e4e6 100644 --- a/definitions/tools/filter_vcf_coding_variant.wdl +++ b/definitions/tools/filter_vcf_coding_variant.wdl @@ -7,6 +7,8 @@ task filterVcfCodingVariant { Int space_needed_gb = 10 + round(2*size(vcf, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "mgibio/vep_helper-cwl:vep_105.0_v1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_vcf_custom_allele_freq.wdl b/definitions/tools/filter_vcf_custom_allele_freq.wdl index 5b07e37c..9afd684d 100644 --- a/definitions/tools/filter_vcf_custom_allele_freq.wdl +++ b/definitions/tools/filter_vcf_custom_allele_freq.wdl @@ -9,6 +9,8 @@ task filterVcfCustomAlleleFreq { Int space_needed_gb = 10 + round(size(vcf, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/vep_helper-cwl:vep_105.0_v1" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_vcf_depth.wdl b/definitions/tools/filter_vcf_depth.wdl index 8fd76069..48aa688c 100644 --- a/definitions/tools/filter_vcf_depth.wdl +++ b/definitions/tools/filter_vcf_depth.wdl @@ -9,6 +9,8 @@ task filterVcfDepth { Int space_needed_gb = 10 + round(size(vcf, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/depth-filter:0.1.2" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_vcf_docm.wdl b/definitions/tools/filter_vcf_docm.wdl index fbd4b932..8f1b2836 100644 --- a/definitions/tools/filter_vcf_docm.wdl +++ b/definitions/tools/filter_vcf_docm.wdl @@ -10,6 +10,8 @@ task filterVcfDocm { Int space_needed_gb = 10 + round(size(docm_raw_variants, "GB")*2 + size([normal_bam, tumor_bam], "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/cle:v1.4.2" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/filter_vcf_mapq0.wdl b/definitions/tools/filter_vcf_mapq0.wdl index f75d950a..cd047c5c 100644 --- a/definitions/tools/filter_vcf_mapq0.wdl +++ b/definitions/tools/filter_vcf_mapq0.wdl @@ -12,6 +12,8 @@ task filterVcfMapq0 { Float bam_size = size([tumor_bam, tumor_bam_bai], "GB") Int space_needed_gb = 10 + round(bam_size + 2*size(vcf, "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/mapq0-filter:v0.5.3" memory: "8GB" bootDiskSizeGb: 10 diff --git a/definitions/tools/filter_vcf_somatic_llr.wdl b/definitions/tools/filter_vcf_somatic_llr.wdl index 0a33c7bf..5cc9e28a 100644 --- a/definitions/tools/filter_vcf_somatic_llr.wdl +++ b/definitions/tools/filter_vcf_somatic_llr.wdl @@ -12,6 +12,8 @@ task filterVcfSomaticLlr { Int space_needed_gb = 10 + round(size(vcf, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/somatic-llr-filter:v0.4.3" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/fp_filter.wdl b/definitions/tools/fp_filter.wdl index 2cd3a9a0..9d151123 100644 --- a/definitions/tools/fp_filter.wdl +++ b/definitions/tools/fp_filter.wdl @@ -16,6 +16,8 @@ task fpFilter { Int space_needed_gb = 10 + round(size(vcf, "GB")*2 + size([reference, reference_fai, reference_dict, bam], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "6GB" bootDiskSizeGb: 25 docker: "mgibio/fp_filter-cwl:1.0.1" diff --git a/definitions/tools/freemix.wdl b/definitions/tools/freemix.wdl index b3116e12..a3afac4f 100644 --- a/definitions/tools/freemix.wdl +++ b/definitions/tools/freemix.wdl @@ -6,6 +6,8 @@ task freemix { } runtime { + preemptible: 1 + maxRetries: 2 docker: "python:3.10" } diff --git a/definitions/tools/gatk_haplotype_caller.wdl b/definitions/tools/gatk_haplotype_caller.wdl index e0239693..7d4b8903 100644 --- a/definitions/tools/gatk_haplotype_caller.wdl +++ b/definitions/tools/gatk_haplotype_caller.wdl @@ -24,6 +24,8 @@ task gatkHaplotypeCaller { Float vcf_size = size([dbsnp_vcf, dbsnp_vcf_tbi], "GB") Int space_needed_gb = 10 + round(reference_size + 2*bam_size + vcf_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "18GB" docker: "broadinstitute/gatk:4.1.8.1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/generate_qc_metrics.wdl b/definitions/tools/generate_qc_metrics.wdl index b5a52fc9..0d659c62 100644 --- a/definitions/tools/generate_qc_metrics.wdl +++ b/definitions/tools/generate_qc_metrics.wdl @@ -10,6 +10,8 @@ task generateQcMetrics { Int space_needed_gb = 10 + round(size([bam, refFlat, ribosomal_intervals], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "18GB" docker: "mgibio/rnaseq:1.0.0" cpu: 1 diff --git a/definitions/tools/germline_combine_variants.wdl b/definitions/tools/germline_combine_variants.wdl index 7476064b..39eaac6d 100644 --- a/definitions/tools/germline_combine_variants.wdl +++ b/definitions/tools/germline_combine_variants.wdl @@ -15,6 +15,8 @@ task germlineCombineVariants { Float vcf_size = size([varscan_vcf, varscan_vcf_tbi, docm_vcf, docm_vcf_tbi], "GB") Int space_needed_gb = 10 + round(reference_size + 2*vcf_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "9GB" bootDiskSizeGb: 25 docker: "mgibio/gatk-cwl:3.6.0" diff --git a/definitions/tools/hisat2_align.wdl b/definitions/tools/hisat2_align.wdl index 47dd3a98..b68cc35c 100644 --- a/definitions/tools/hisat2_align.wdl +++ b/definitions/tools/hisat2_align.wdl @@ -33,6 +33,8 @@ task hisat2Align { ], "GB") Int space_needed_gb = 10 + round(5*fastq_size_gb + reference_size_gb) runtime { + preemptible: 1 + maxRetries: 2 memory: "32GB" cpu: cores bootDiskSizeGb: space_needed_gb diff --git a/definitions/tools/hla_consensus.wdl b/definitions/tools/hla_consensus.wdl index c09376ba..68d3c94f 100644 --- a/definitions/tools/hla_consensus.wdl +++ b/definitions/tools/hla_consensus.wdl @@ -9,6 +9,8 @@ task hlaConsensus { } runtime { + preemptible: 1 + maxRetries: 2 docker: "python:3.7.4-slim-buster" memory: "4GB" } diff --git a/definitions/tools/index_bam.wdl b/definitions/tools/index_bam.wdl index f1504fea..d4c3726a 100644 --- a/definitions/tools/index_bam.wdl +++ b/definitions/tools/index_bam.wdl @@ -5,6 +5,8 @@ task indexBam { Int space_needed_gb = 10 + round(size(bam, "GB")*3) 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/index_cram.wdl b/definitions/tools/index_cram.wdl index 2eff0f8e..7bb59b38 100644 --- a/definitions/tools/index_cram.wdl +++ b/definitions/tools/index_cram.wdl @@ -5,6 +5,8 @@ task indexCram { Int space_needed_gb = 10 + round(size(cram, "GB")*3) 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/index_vcf.wdl b/definitions/tools/index_vcf.wdl index da7d96f2..4a1e3f82 100644 --- a/definitions/tools/index_vcf.wdl +++ b/definitions/tools/index_vcf.wdl @@ -7,6 +7,8 @@ task indexVcf { Int space_needed_gb = 10 + round(3*size(vcf, "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/intersect_known_variants.wdl b/definitions/tools/intersect_known_variants.wdl index bfeb02cb..e8f0fa97 100644 --- a/definitions/tools/intersect_known_variants.wdl +++ b/definitions/tools/intersect_known_variants.wdl @@ -10,6 +10,8 @@ task intersectKnownVariants { Int space_needed_gb = 10 + round(2*size([vcf, vcf_tbi, validated_variants, validated_variants_tbi], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "8GB" docker: "mgibio/bcftools-cwl:1.12" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/interval_list_expand.wdl b/definitions/tools/interval_list_expand.wdl index 8d24bd07..72fcfdeb 100644 --- a/definitions/tools/interval_list_expand.wdl +++ b/definitions/tools/interval_list_expand.wdl @@ -8,6 +8,8 @@ task intervalListExpand { Int space_needed_gb = 10 + round(size(interval_list, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "broadinstitute/picard:2.23.6" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/intervals_to_bed.wdl b/definitions/tools/intervals_to_bed.wdl index 84480cee..fd97ceae 100644 --- a/definitions/tools/intervals_to_bed.wdl +++ b/definitions/tools/intervals_to_bed.wdl @@ -6,6 +6,8 @@ task intervalsToBed { } runtime { + preemptible: 1 + maxRetries: 2 docker: "ubuntu:bionic" memory: "4GB" } diff --git a/definitions/tools/kallisto.wdl b/definitions/tools/kallisto.wdl index fe5049fd..e4a8a82d 100644 --- a/definitions/tools/kallisto.wdl +++ b/definitions/tools/kallisto.wdl @@ -10,6 +10,8 @@ task kallisto { Int cores = 8 Int space_needed_gb = 10 + round(size(flatten(fastqs), "GB") + size(kallisto_index, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "32GB" cpu: cores docker: "quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0" diff --git a/definitions/tools/manta_somatic.wdl b/definitions/tools/manta_somatic.wdl index 6d22d2a8..606c5608 100644 --- a/definitions/tools/manta_somatic.wdl +++ b/definitions/tools/manta_somatic.wdl @@ -21,6 +21,8 @@ task mantaSomatic { Float regions_size = size([call_regions, call_regions_tbi], "GB") Int size_needed_gb = 10 + 2 * round(ref_size + bam_size + regions_size) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/manta_somatic-cwl:1.6.0" cpu: cores memory: "24GB" diff --git a/definitions/tools/mark_duplicates_and_sort.wdl b/definitions/tools/mark_duplicates_and_sort.wdl index a1e2266b..02bb662d 100644 --- a/definitions/tools/mark_duplicates_and_sort.wdl +++ b/definitions/tools/mark_duplicates_and_sort.wdl @@ -11,6 +11,8 @@ task markDuplicatesAndSort { #markdup is listed as 2Gb per 100M reads Int mem_needed_gb = round(((size(bam, "GB")*15)/100)*2)+32 runtime { + preemptible: 1 + maxRetries: 2 docker: "quay.io/biocontainers/sambamba:0.8.2--h98b6b92_2" memory: "~{mem_needed_gb}GB" cpu: 16 diff --git a/definitions/tools/merge_bams.wdl b/definitions/tools/merge_bams.wdl index c3809edd..8bfd516f 100644 --- a/definitions/tools/merge_bams.wdl +++ b/definitions/tools/merge_bams.wdl @@ -10,6 +10,8 @@ task mergeBams { Int cores = 4 Int space_needed_gb = 10 + round(4*size(bams, "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/bam-merge:0.1" memory: "8GB" cpu: cores diff --git a/definitions/tools/merge_vcf.wdl b/definitions/tools/merge_vcf.wdl index bd1ce1e0..d35f8481 100644 --- a/definitions/tools/merge_vcf.wdl +++ b/definitions/tools/merge_vcf.wdl @@ -9,6 +9,8 @@ task mergeVcf { Int space_needed_gb = 10 + round(2*(size(vcfs, "GB") + size(vcf_tbis, "GB"))) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/bcftools-cwl:1.12" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/mutect.wdl b/definitions/tools/mutect.wdl index 57c3d6b3..a165b8f9 100644 --- a/definitions/tools/mutect.wdl +++ b/definitions/tools/mutect.wdl @@ -26,6 +26,8 @@ task mutect { Float bam_size = size([tumor_bam, tumor_bam_bai, normal_bam, normal_bam_bai], "GB") Int space_needed_gb = 10 + ceil(reference_size + 2*bam_size + size(interval_list, "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "broadinstitute/gatk:4.2.3.0" memory: "2GB" bootDiskSizeGb: space_needed_gb diff --git a/definitions/tools/name_sort.wdl b/definitions/tools/name_sort.wdl index 2c3924b6..0b28886e 100644 --- a/definitions/tools/name_sort.wdl +++ b/definitions/tools/name_sort.wdl @@ -9,6 +9,8 @@ task nameSort { Int input_size_gb = 10 + 5*round(size(bam, "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/sambamba-cwl:0.6.4" memory: "26GB" cpu: cores diff --git a/definitions/tools/normalize_variants.wdl b/definitions/tools/normalize_variants.wdl index 42e9d42a..1442fefe 100644 --- a/definitions/tools/normalize_variants.wdl +++ b/definitions/tools/normalize_variants.wdl @@ -12,6 +12,8 @@ task normalizeVariants { Int space_needed_gb = 10 + round(size([vcf, vcf_tbi], "GB") + size([reference, reference_fai, reference_dict], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "9GB" docker: "broadinstitute/gatk:4.1.8.1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/optitype_dna.wdl b/definitions/tools/optitype_dna.wdl index d8455ea8..cc5d4db6 100644 --- a/definitions/tools/optitype_dna.wdl +++ b/definitions/tools/optitype_dna.wdl @@ -13,6 +13,8 @@ task optitypeDna { Int space_needed_gb = 10 + round(5*size([cram, cram_crai, reference, reference_fai], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "~{mem}GB" cpu: threads docker: "mgibio/immuno_tools-cwl:1.0.2" diff --git a/definitions/tools/phlat.wdl b/definitions/tools/phlat.wdl index 2d2e84ee..8e7afe25 100644 --- a/definitions/tools/phlat.wdl +++ b/definitions/tools/phlat.wdl @@ -14,6 +14,8 @@ task phlat { Int space_needed_gb = 10 + round(5*size([cram, cram_crai, reference, reference_fai], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "~{mem}GB" cpu: nthreads docker: "mgibio/phlat:1.1_withindex" diff --git a/definitions/tools/picard_merge_vcfs.wdl b/definitions/tools/picard_merge_vcfs.wdl index 84e26e2e..441c6f6e 100644 --- a/definitions/tools/picard_merge_vcfs.wdl +++ b/definitions/tools/picard_merge_vcfs.wdl @@ -9,6 +9,8 @@ task picardMergeVcfs { Int space_needed_gb = 10 + round(size(sequence_dictionary, "GB") + size(vcfs, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "40GB" docker: "broadinstitute/gatk:4.1.8.1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/pindel.wdl b/definitions/tools/pindel.wdl index 024f3f3b..eeee772e 100644 --- a/definitions/tools/pindel.wdl +++ b/definitions/tools/pindel.wdl @@ -19,6 +19,8 @@ task pindel { Int cores = 4 Int space_needed_gb = 10 + round(size([reference, reference_fai, reference_dict, normal_bam, normal_bam_bai, tumor_bam, tumor_bam_bai, region_file], "GB")) runtime { + preemptible: 1 + maxRetries: 2 bootDiskSizeGb: 100 cpu: cores disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/pindel_somatic_filter.wdl b/definitions/tools/pindel_somatic_filter.wdl index d0ce1112..ed021db6 100644 --- a/definitions/tools/pindel_somatic_filter.wdl +++ b/definitions/tools/pindel_somatic_filter.wdl @@ -10,6 +10,8 @@ task pindelSomaticFilter { Int space_needed_gb = 10 + round(size([reference, reference_fai, reference_dict, pindel_output_summary], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" docker: "mgibio/cle:v1.3.1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/pvacfuse.wdl b/definitions/tools/pvacfuse.wdl index 1d39edec..351145ac 100644 --- a/definitions/tools/pvacfuse.wdl +++ b/definitions/tools/pvacfuse.wdl @@ -27,6 +27,8 @@ task pvacfuse { Int space_needed_gb = 10 + round(size([input_fusions_zip], "GB") * 3) runtime { + preemptible: 1 + maxRetries: 2 docker: "griffithlab/pvactools:3.1.0" memory: "16GB" cpu: n_threads diff --git a/definitions/tools/pvacseq.wdl b/definitions/tools/pvacseq.wdl index 49b84747..44227bfb 100644 --- a/definitions/tools/pvacseq.wdl +++ b/definitions/tools/pvacseq.wdl @@ -48,6 +48,8 @@ task pvacseq { Float phased_variants_size = size([phased_proximal_variants_vcf, phased_proximal_variants_vcf_tbi], "GB") Int space_needed_gb = 10 + round(input_size + phased_variants_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" cpu: n_threads docker: "griffithlab/pvactools:3.1.0" diff --git a/definitions/tools/pvacseq_combine_variants.wdl b/definitions/tools/pvacseq_combine_variants.wdl index ab1a5935..3861097a 100644 --- a/definitions/tools/pvacseq_combine_variants.wdl +++ b/definitions/tools/pvacseq_combine_variants.wdl @@ -15,6 +15,8 @@ task pvacseqCombineVariants { Float vcf_size = size([germline_vcf, germline_vcf_tbi, somatic_vcf, somatic_vcf_tbi], "GB") Int space_needed_gb = 10 + round(reference_size + 2*vcf_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "9GB" bootDiskSizeGb: 25 docker: "mgibio/gatk-cwl:3.6.0" diff --git a/definitions/tools/read_backed_phasing.wdl b/definitions/tools/read_backed_phasing.wdl index 320cc666..15ac0758 100644 --- a/definitions/tools/read_backed_phasing.wdl +++ b/definitions/tools/read_backed_phasing.wdl @@ -13,6 +13,8 @@ task readBackedPhasing { Int space_needed_gb = 10 + round(size([bam, bam_index, reference, reference_fai, reference_dict, vcf, vcf_tbi], "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/gatk-cwl:3.6.0" memory: "9GB" bootDiskSizeGb: 25 diff --git a/definitions/tools/remove_end_tags.wdl b/definitions/tools/remove_end_tags.wdl index b5ce7bba..8996c9ee 100644 --- a/definitions/tools/remove_end_tags.wdl +++ b/definitions/tools/remove_end_tags.wdl @@ -8,6 +8,8 @@ task removeEndTags { Int space_needed_gb = 10 + round(size(vcf, "GB")*2) 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/replace_vcf_sample_name.wdl b/definitions/tools/replace_vcf_sample_name.wdl index 4580bc41..e6defb96 100644 --- a/definitions/tools/replace_vcf_sample_name.wdl +++ b/definitions/tools/replace_vcf_sample_name.wdl @@ -9,6 +9,8 @@ task replaceVcfSampleName { Int space_needed_gb = 10 + round(size(input_vcf, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "8GB" docker: "mgibio/bcftools-cwl:1.12" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/samtools_flagstat.wdl b/definitions/tools/samtools_flagstat.wdl index 951fe009..71938132 100644 --- a/definitions/tools/samtools_flagstat.wdl +++ b/definitions/tools/samtools_flagstat.wdl @@ -13,6 +13,8 @@ task samtoolsFlagstat { Int space_needed_gb = 10 + round(size([bam, bam_bai], "GB")*2) 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/samtools_sort.wdl b/definitions/tools/samtools_sort.wdl index f9e4edde..65c779f5 100644 --- a/definitions/tools/samtools_sort.wdl +++ b/definitions/tools/samtools_sort.wdl @@ -9,6 +9,8 @@ task samtoolsSort { Int cores = 1 Int space_needed_gb = 10 + round(3*size(input_bam, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" cpu: cores docker: "quay.io/biocontainers/samtools:1.11--h6270b1f_0" diff --git a/definitions/tools/select_variants.wdl b/definitions/tools/select_variants.wdl index 9f5e83bb..cae794bc 100644 --- a/definitions/tools/select_variants.wdl +++ b/definitions/tools/select_variants.wdl @@ -25,6 +25,8 @@ task selectVariants { Int space_needed_gb = 10 + round(size([vcf, vcf_tbi], "GB")*3 + size([reference, reference_fai, reference_dict, interval_list], "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "broadinstitute/gatk:4.1.8.1" memory: "6GB" bootDiskSizeGb: 25 diff --git a/definitions/tools/sequence_align_and_tag.wdl b/definitions/tools/sequence_align_and_tag.wdl index e5a41ce1..bff9d292 100644 --- a/definitions/tools/sequence_align_and_tag.wdl +++ b/definitions/tools/sequence_align_and_tag.wdl @@ -28,6 +28,8 @@ task sequenceAlignAndTag { Int instance_memory_gb = 76 Int jvm_memory_gb = 4 runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/alignment_helper-cwl:2.2.1" memory: "~{instance_memory_gb}GB" cpu: cores diff --git a/definitions/tools/sequence_to_fastq.wdl b/definitions/tools/sequence_to_fastq.wdl index 99a05ec5..8ea3326d 100644 --- a/definitions/tools/sequence_to_fastq.wdl +++ b/definitions/tools/sequence_to_fastq.wdl @@ -13,6 +13,8 @@ task sequenceToFastq { Int compression_multiplier = if unzip_fastqs then 10 else 1 Int space_needed_gb = 10 + ceil(2*compression_multiplier*size([bam, fastq1, fastq2], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" bootDiskSizeGb: 25 docker: "broadinstitute/picard:2.23.6" diff --git a/definitions/tools/set_filter_status.wdl b/definitions/tools/set_filter_status.wdl index 31a823fb..0c00730a 100644 --- a/definitions/tools/set_filter_status.wdl +++ b/definitions/tools/set_filter_status.wdl @@ -15,6 +15,8 @@ task setFilterStatus { Float reference_size = size([reference, reference_fai, reference_dict], "GB") Int space_needed_gb = 10 + round(reference_size + vcf_size*2) runtime { + preemptible: 1 + maxRetries: 2 disks: "local-disk ~{space_needed_gb} HDD" memory: "6GB" bootDiskSizeGb: 25 diff --git a/definitions/tools/single_sample_docm_filter.wdl b/definitions/tools/single_sample_docm_filter.wdl index 929d04cb..db1433ac 100644 --- a/definitions/tools/single_sample_docm_filter.wdl +++ b/definitions/tools/single_sample_docm_filter.wdl @@ -7,6 +7,8 @@ task singleSampleDocmFilter { Int space_needed_gb = 10 + round(size(docm_out, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "mgibio/perl_helper-cwl:1.0.0" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/smoove.wdl b/definitions/tools/smoove.wdl index 21739acf..317422be 100644 --- a/definitions/tools/smoove.wdl +++ b/definitions/tools/smoove.wdl @@ -14,6 +14,8 @@ task smoove { Float reference_size = size([reference, reference_fai, reference_dict], "GB") Int space_needed_gb = 10 + round(2*(size(bams, "GB") + reference_size)) runtime { + preemptible: 1 + maxRetries: 2 memory: "20GB" cpu: cores bootDiskSizeGb: 10 diff --git a/definitions/tools/sort_vcf.wdl b/definitions/tools/sort_vcf.wdl index 7265b1fa..64adef89 100644 --- a/definitions/tools/sort_vcf.wdl +++ b/definitions/tools/sort_vcf.wdl @@ -8,6 +8,8 @@ task sortVcf { Int space_needed_gb = 10 + round(size(vcf, "GB") + size(reference_dict, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "18GB" docker: "broadinstitute/picard:2.23.6" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/split_interval_list.wdl b/definitions/tools/split_interval_list.wdl index 06db8ef2..fc088b8d 100644 --- a/definitions/tools/split_interval_list.wdl +++ b/definitions/tools/split_interval_list.wdl @@ -8,6 +8,8 @@ task splitIntervalList { Int space_needed_gb = 10 + round(size(interval_list, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 docker: "broadinstitute/picard:2.24.2" memory: "6GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/split_interval_list_to_bed.wdl b/definitions/tools/split_interval_list_to_bed.wdl index 9212178e..c5e71bd0 100644 --- a/definitions/tools/split_interval_list_to_bed.wdl +++ b/definitions/tools/split_interval_list_to_bed.wdl @@ -8,6 +8,8 @@ task splitIntervalListToBed { Int space_needed_gb = 10 + round(size(interval_list, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "6GB" docker: "mgibio/cle:v1.4.2" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/staged_rename.wdl b/definitions/tools/staged_rename.wdl index 3476d859..62ba2b44 100644 --- a/definitions/tools/staged_rename.wdl +++ b/definitions/tools/staged_rename.wdl @@ -8,6 +8,8 @@ task stagedRename { Int space_needed_gb = 10 + round(size(original, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" cpu: 1 docker: "ubuntu:bionic" diff --git a/definitions/tools/star_align_fusion.wdl b/definitions/tools/star_align_fusion.wdl index 5896877e..750f873a 100644 --- a/definitions/tools/star_align_fusion.wdl +++ b/definitions/tools/star_align_fusion.wdl @@ -37,6 +37,8 @@ task starAlignFusion { Float fastq_size = size(flatten([fastq, fastq2]), "GB") Int space_needed_gb = 10 + round(2 * (zip_size + fastq_size)) runtime { + preemptible: 1 + maxRetries: 2 cpu: cores memory: "64GB" docker: "trinityctat/starfusion:1.10.1" diff --git a/definitions/tools/star_fusion_detect.wdl b/definitions/tools/star_fusion_detect.wdl index 8b35b4aa..07b0c71d 100644 --- a/definitions/tools/star_fusion_detect.wdl +++ b/definitions/tools/star_fusion_detect.wdl @@ -18,6 +18,8 @@ task starFusionDetect { Float fastq_size = size(flatten([fastq, fastq2]), "GB") Int space_needed_gb = 10 + round(3 * (zip_size + fastq_size)) runtime { + preemptible: 1 + maxRetries: 2 memory: "64GB" cpu: cores docker: "trinityctat/starfusion:pre-1.11.c" diff --git a/definitions/tools/strandedness_check.wdl b/definitions/tools/strandedness_check.wdl index 13f6d577..e211221c 100644 --- a/definitions/tools/strandedness_check.wdl +++ b/definitions/tools/strandedness_check.wdl @@ -11,6 +11,8 @@ task strandednessCheck { Int space_needed_gb = 10 + round(2*size([reference_annotation, kallisto_index, cdna_fasta, reads1, reads2], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" bootDiskSizeGb: space_needed_gb # default cpu: 1 diff --git a/definitions/tools/strelka.wdl b/definitions/tools/strelka.wdl index 9d638fd8..dc11fffc 100644 --- a/definitions/tools/strelka.wdl +++ b/definitions/tools/strelka.wdl @@ -21,6 +21,8 @@ task strelka { Float bam_size = size([tumor_bam, tumor_bam_bai, normal_bam, normal_bam_bai], "GB") Int space_needed_gb = 10 + round(bam_size*2 + reference_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" cpu: 4 docker: "mgibio/strelka-cwl:2.9.9" diff --git a/definitions/tools/stringtie.wdl b/definitions/tools/stringtie.wdl index d8ef7875..29a3b7e5 100644 --- a/definitions/tools/stringtie.wdl +++ b/definitions/tools/stringtie.wdl @@ -11,6 +11,8 @@ task stringtie { Int cores = 12 Int space_needed_gb = 10 + round(size([bam, reference_annotation], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" cpu: cores docker: "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0" diff --git a/definitions/tools/survivor.wdl b/definitions/tools/survivor.wdl index 6f798f73..5726f4a1 100644 --- a/definitions/tools/survivor.wdl +++ b/definitions/tools/survivor.wdl @@ -14,6 +14,8 @@ task survivor { Int space_needed_gb = 10 runtime { + preemptible: 1 + maxRetries: 2 docker: "mgibio/survivor-cwl:1.0.6.2" memory: "2GB" cpu: 1 diff --git a/definitions/tools/transcript_to_gene.wdl b/definitions/tools/transcript_to_gene.wdl index fe6be342..c44eba4e 100644 --- a/definitions/tools/transcript_to_gene.wdl +++ b/definitions/tools/transcript_to_gene.wdl @@ -8,6 +8,8 @@ task transcriptToGene { Int space_needed_gb = 10 + round(size([transcript_table_h5, gene_transcript_lookup_table], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "2GB" cpu: 1 docker: "mgibio/rnaseq:1.0.0" diff --git a/definitions/tools/trim_fastq.wdl b/definitions/tools/trim_fastq.wdl index f43ccb3d..d22ddf70 100644 --- a/definitions/tools/trim_fastq.wdl +++ b/definitions/tools/trim_fastq.wdl @@ -14,6 +14,8 @@ task trimFastq { Int cores = 4 Int space_needed_gb = 10 + ceil(size(adapters, "GB") + 10*size([reads1, reads2], "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "16GB" bootDiskSizeGb: 25 cpu: 4 diff --git a/definitions/tools/variants_to_table.wdl b/definitions/tools/variants_to_table.wdl index 82cc06ae..0b60d9b5 100644 --- a/definitions/tools/variants_to_table.wdl +++ b/definitions/tools/variants_to_table.wdl @@ -20,6 +20,8 @@ task variantsToTable { Float vcf_size = size([vcf, vcf_tbi], "GB") Int space_needed_gb = 10 + round(vcf_size*2 + reference_size) runtime { + preemptible: 1 + maxRetries: 2 memory: "6GB" bootDiskSizeGb: 25 docker: "broadinstitute/gatk:4.1.8.1" diff --git a/definitions/tools/varscan_germline.wdl b/definitions/tools/varscan_germline.wdl index cdeb6303..8103a25f 100644 --- a/definitions/tools/varscan_germline.wdl +++ b/definitions/tools/varscan_germline.wdl @@ -18,6 +18,8 @@ task varscanGermline { Int space_needed_gb = 10 runtime { + preemptible: 1 + maxRetries: 2 memory: "12GB" cpu: 2 docker: "mgibio/varscan_helper-cwl:1.0.0" diff --git a/definitions/tools/varscan_process_somatic.wdl b/definitions/tools/varscan_process_somatic.wdl index bcdb3857..993f1567 100644 --- a/definitions/tools/varscan_process_somatic.wdl +++ b/definitions/tools/varscan_process_somatic.wdl @@ -8,6 +8,8 @@ task varscanProcessSomatic { Int space_needed_gb = 10 + round(size(variants, "GB")*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" docker: "mgibio/cle:v1.3.1" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/varscan_somatic.wdl b/definitions/tools/varscan_somatic.wdl index 43b4f81c..d830b590 100644 --- a/definitions/tools/varscan_somatic.wdl +++ b/definitions/tools/varscan_somatic.wdl @@ -23,6 +23,8 @@ task varscanSomatic { Float bam_size = size([tumor_bam, tumor_bam_bai, normal_bam, normal_bam_bai], "GB") Int space_needed_gb = 10 + ceil(reference_size + bam_size*2) runtime { + preemptible: 1 + maxRetries: 2 memory: "12GB" cpu: 2 docker: "mgibio/cle:v1.3.1" diff --git a/definitions/tools/vcf_expression_annotator.wdl b/definitions/tools/vcf_expression_annotator.wdl index 4aecfa0d..605b9283 100644 --- a/definitions/tools/vcf_expression_annotator.wdl +++ b/definitions/tools/vcf_expression_annotator.wdl @@ -11,6 +11,8 @@ task vcfExpressionAnnotator { Int space_needed_gb = 10 + round(2*size([vcf, expression_file], "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "griffithlab/vatools:4.1.0" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/vcf_readcount_annotator.wdl b/definitions/tools/vcf_readcount_annotator.wdl index a67ef462..4ed3dcce 100644 --- a/definitions/tools/vcf_readcount_annotator.wdl +++ b/definitions/tools/vcf_readcount_annotator.wdl @@ -11,6 +11,8 @@ task vcfReadcountAnnotator { Int space_needed_gb = 10 + round(size(vcf, "GB")*2 + size(bam_readcount_tsv, "GB")) runtime { + preemptible: 1 + maxRetries: 2 docker: "griffithlab/vatools:4.1.0" memory: "4GB" disks: "local-disk ~{space_needed_gb} HDD" diff --git a/definitions/tools/vcf_sanitize.wdl b/definitions/tools/vcf_sanitize.wdl index f26d04af..bbba3034 100644 --- a/definitions/tools/vcf_sanitize.wdl +++ b/definitions/tools/vcf_sanitize.wdl @@ -6,6 +6,8 @@ task vcfSanitize { } runtime { + preemptible: 1 + maxRetries: 2 memory: "4GB" cpu: 1 docker: "mgibio/samtools-cwl:1.0.0" diff --git a/definitions/tools/vep.wdl b/definitions/tools/vep.wdl index c8aa97f6..7cf37928 100644 --- a/definitions/tools/vep.wdl +++ b/definitions/tools/vep.wdl @@ -31,6 +31,8 @@ task vepTask { Float reference_size = size([reference, reference_fai, reference_dict], "GB") Int space_needed_gb = 10 + round(reference_size + vcf_size + cache_size + size(synonyms_file, "GB")) runtime { + preemptible: 1 + maxRetries: 2 memory: "64GB" bootDiskSizeGb: 30 cpu: 4 @@ -83,7 +85,11 @@ task vepTask { # happen in WDL instead of a task task parseVepCustomAnnotationIntoArg { input { VepCustomAnnotation obj } - runtime { docker: "python:3.10" } + runtime { + preemptible: 1 + maxRetries: 2 + docker: "python:3.10" + } command <<< python <