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change runtime attrs to args #8413

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merged 11 commits into from
Jul 11, 2023
Merged

change runtime attrs to args #8413

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e51b1cf
updated RevertSam disk_size attribute
dyeramosu Jul 11, 2023
7f42359
updated CoverageAtEveryBase disk_size attr
dyeramosu Jul 11, 2023
030f171
updated CollectWgsMetrics disk_size attr
dyeramosu Jul 11, 2023
4b604e5
updated M2 task runtime attrs
dyeramosu Jul 11, 2023
eaaa1f4
updated runtime attrs for AlignAndMarkDuplicates
dyeramosu Jul 11, 2023
fa7ebab
updated memory attributes
dyeramosu Jul 11, 2023
1a1d164
updated memory attributes
dyeramosu Jul 11, 2023
72b8cc4
updated runtime attributes
dyeramosu Jul 11, 2023
075a711
cleaned up
dyeramosu Jul 11, 2023
f64adbb
cleaned up
dyeramosu Jul 11, 2023
a8810f2
made requested changes
dyeramosu Jul 11, 2023
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5 changes: 3 additions & 2 deletions scripts/mitochondria_m2_wdl/AlignAndCall.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -430,15 +430,16 @@ task M2 {

# runtime
String? gatk_docker_override
Int mem
Int? mem
Int? preemptible_tries
Int disk_size = ceil(size(input_bam, "GB") + size(ref_fasta, "GB") + size(ref_fai, "GB")) + 20
Int machine_mem = if defined(mem) then mem * 1000 else 3500 # Mem is in units of GB but our command and memory runtime values are in MB
}

String output_vcf = "raw" + if compress then ".vcf.gz" else ".vcf"
String output_vcf_index = output_vcf + if compress then ".tbi" else ".idx"

# Mem is in units of GB but our command and memory runtime values are in MB
Int machine_mem = if defined(mem) then mem * 1000 else 3500
Int command_mem = machine_mem - 500
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@meganshand pushed new changes, let me know how this looks!


meta {
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3 changes: 1 addition & 2 deletions scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
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Expand Up @@ -253,7 +253,6 @@ task RevertSam {
Int? preemptible_tries
Int machine_mem = 2000
Int disk_size = ceil(size(input_bam, "GB") * 2.5) + 20
Int mem = machine_mem
}
Int java_mem = machine_mem - 1000

Expand All @@ -277,7 +276,7 @@ task RevertSam {
}
runtime {
disks: "local-disk " + disk_size + " HDD"
memory: mem + " MB"
memory: machine_mem + " MB"
docker: "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.2-1552931386"
preemptible: select_first([preemptible_tries, 5])
}
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