Increased minimum boot disk size to 25Gb for all tasks. (#476)

Fixed critical issue with boot disk size in Terra. Google likely changed their image and the boot disk is no longer big enough. Updated boot disk sizes to be 25 gb (or larger) by default.
broadinstitute · Nov 20, 2024 · 60a7e5e · 60a7e5e
1 parent 86388fc
commit 60a7e5e
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Showing 85 changed files with 346 additions and 346 deletions.
diff --git a/wdl/deprecated/DownloadFromHudsonAlpha.wdl b/wdl/deprecated/DownloadFromHudsonAlpha.wdl
@@ -71,7 +71,7 @@ task GetFileSize {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            1,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:0.2.3"
@@ -115,7 +115,7 @@ task DownloadFile {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:0.2.3"
@@ -170,7 +170,7 @@ task VerifyAndExtractTarball {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:0.2.3"
@@ -224,7 +224,7 @@ task ExtractFiles {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-cloud-downloader:0.2.3"

diff --git a/wdl/deprecated/ONT10x.wdl b/wdl/deprecated/ONT10x.wdl
@@ -307,7 +307,7 @@ task AnnotateAdapters {
         cpu_cores:          cpus,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-10x:0.1.9"
@@ -349,7 +349,7 @@ task CountNumPasses {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -399,7 +399,7 @@ task FastaToSam {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -455,7 +455,7 @@ task CountFastqRecords {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -506,7 +506,7 @@ task CountFastaRecords {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"

diff --git a/wdl/deprecated/PBCCS10x.wdl b/wdl/deprecated/PBCCS10x.wdl
@@ -215,7 +215,7 @@ task GrepCountBamRecords {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -266,7 +266,7 @@ task BamToTable {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"

diff --git a/wdl/deprecated/PreprocessBarcodedCCSedSMRTCell.wdl b/wdl/deprecated/PreprocessBarcodedCCSedSMRTCell.wdl
@@ -402,7 +402,7 @@ task FixSampleName {
         cpu_cores:          1,
         mem_gb:             4,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-basic:0.1.1"

diff --git a/wdl/deprecated/TestCromwell.wdl b/wdl/deprecated/TestCromwell.wdl
@@ -30,7 +30,7 @@ task TestCromwellOnGCS {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            1,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"

diff --git a/wdl/deprecated/tasks/AnnotateAdapters.wdl b/wdl/deprecated/tasks/AnnotateAdapters.wdl
@@ -44,7 +44,7 @@ task AnnotateAdapters {
         cpu_cores:          cpus,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-10x:0.1.9"

diff --git a/wdl/deprecated/tasks/Busco.wdl b/wdl/deprecated/tasks/Busco.wdl
@@ -26,7 +26,7 @@ task Busco {
         cpu_cores:      8,
         mem_gb:         32,
         disk_gb:        50,
-        boot_disk_gb:   10,
+        boot_disk_gb:   25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "ezlabgva/busco:v4.1.1_cv1"

diff --git a/wdl/deprecated/tasks/C3POa.wdl b/wdl/deprecated/tasks/C3POa.wdl
@@ -81,7 +81,7 @@ task Processing {
         cpu_cores:          1,
         mem_gb:             8,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-c3poa:2.2.2"
@@ -124,7 +124,7 @@ task Postprocessing {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-c3poa:0.1.9"
@@ -166,7 +166,7 @@ task Cat {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-c3poa:0.1.9"

diff --git a/wdl/deprecated/tasks/CCSLima.wdl b/wdl/deprecated/tasks/CCSLima.wdl
@@ -106,7 +106,7 @@ task CCSLima {
         cpu_cores:          16,
         mem_gb:             64,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-pb:0.1.36"
@@ -283,7 +283,7 @@ task MakeSummarizedCustomDemultiplexingReport {
         cpu_cores:          4,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.10"
@@ -328,7 +328,7 @@ task MakeDetailedCustomDemultiplexingReport {
         cpu_cores:          8,
         mem_gb:             32,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.10"
@@ -381,7 +381,7 @@ task MakePerBarcodeCustomDemultiplexingReports {
         cpu_cores:          4,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-metrics:0.1.10"

diff --git a/wdl/deprecated/tasks/CallVariantsPBCLR.wdl b/wdl/deprecated/tasks/CallVariantsPBCLR.wdl
@@ -225,7 +225,7 @@ task CollectDefinitions {
         cpu_cores:          4,
         mem_gb:             16,
         disk_gb:            disk_sz,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-basic:latest"
@@ -418,7 +418,7 @@ task FixSnifflesVCF {
         cpu_cores:          1,
         mem_gb:             3,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  2,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-basic:latest"

diff --git a/wdl/deprecated/tasks/CuteSV.wdl b/wdl/deprecated/tasks/CuteSV.wdl
@@ -75,7 +75,7 @@ task CuteSV {
         cpu_cores:          2,
         mem_gb:             10,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-sv:0.1.8"

diff --git a/wdl/deprecated/tasks/GATKBestPractice.wdl b/wdl/deprecated/tasks/GATKBestPractice.wdl
@@ -281,7 +281,7 @@ task MergeBamouts {
         cpu_cores:          1,
         mem_gb:             4,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsde-methods/samtools-cloud:v1.clean"
@@ -353,7 +353,7 @@ task GenotypeGVCFs {
         cpu_cores:          2,
         mem_gb:             7,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-gatk/gatk:latest"
@@ -405,7 +405,7 @@ task PostProcess {
         cpu_cores:          2,
         mem_gb:             7,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-gatk:0.1.1"

diff --git a/wdl/deprecated/tasks/Longshot.wdl b/wdl/deprecated/tasks/Longshot.wdl
@@ -54,7 +54,7 @@ task Longshot {
         cpu_cores:          4,
         mem_gb:             128,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-longshot:0.4.1"

diff --git a/wdl/deprecated/tasks/Methylation.wdl b/wdl/deprecated/tasks/Methylation.wdl
@@ -94,7 +94,7 @@ task CombineFastqs {
         cpu_cores:          1,
         mem_gb:             1,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -175,7 +175,7 @@ task CallMethylation {
         cpu_cores:          8,
         mem_gb:             64,
         disk_gb:            disk_size,
-        boot_disk_gb:       100,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-methylation:0.1.2"
@@ -227,7 +227,7 @@ task FreqMerge {
         cpu_cores:          1,
         mem_gb:             2,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        2,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-methylation:0.1.0"

diff --git a/wdl/deprecated/tasks/Nanopolish.wdl b/wdl/deprecated/tasks/Nanopolish.wdl
@@ -115,7 +115,7 @@ task NanopolishIndex {
         cpu_cores:          4,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-nanopolish:0.3.0"
@@ -183,7 +183,7 @@ task NanopolishVariants {
         cpu_cores:          4,
         mem_gb:             20,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         # We should try to find a way to support this to reduce costs.
         # Right now, it is almost always preempted with the amount of
         # time it takes to localize the fast5 files
@@ -233,7 +233,7 @@ task MergeVcfs {
         cpu_cores:          4,
         mem_gb:             16,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        1,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-nanopolish:0.3.0"

diff --git a/wdl/deprecated/tasks/Pacasus.wdl b/wdl/deprecated/tasks/Pacasus.wdl
@@ -68,7 +68,7 @@ task SplitReadsByLength {
         cpu:                    4
         memory:                 "8 GiB"
         disks:                  "local-disk " +  disk_size + " HDD"
-        bootDiskSizeGb:         10
+        bootDiskSizeGb:         25
         preemptible:            2
         maxRetries:             0
         docker:                 "quay.io/broad-long-read-pipelines/lr-pacasus:0.3.0"
@@ -100,7 +100,7 @@ task SplitReads {
         cpu:                    4
         memory:                 mem_size + " GiB"
         disks:                  "local-disk " +  disk_size + " HDD"
-        bootDiskSizeGb:         10
+        bootDiskSizeGb:         25
         preemptible:            0
         maxRetries:             0
         docker:                 "quay.io/broad-long-read-pipelines/lr-pacasus:0.3.0"
@@ -130,7 +130,7 @@ task RemovePalindromes {
         cpu_cores:          1,
         mem_gb:             6,
         disk_gb:            disk_size,
-        boot_disk_gb:       15,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0
     }
@@ -171,7 +171,7 @@ task MergeFasta {
         cpu:                    4
         memory:                 "8 GiB"
         disks:                  "local-disk " +  disk_size + " HDD"
-        bootDiskSizeGb:         10
+        bootDiskSizeGb:         25
         preemptible:            2
         maxRetries:             0
         docker:                 "quay.io/broad-long-read-pipelines/lr-pacasus:0.3.0"

diff --git a/wdl/deprecated/tasks/Peregrine.wdl b/wdl/deprecated/tasks/Peregrine.wdl
@@ -85,7 +85,7 @@ task Assemble {
         cpu_cores:          48,
         mem_gb:             384,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  0,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-peregrine:0.1.6"
@@ -128,7 +128,7 @@ task AlignAsPAF {
         cpu_cores:          "~{num_cpus}",
         mem_gb:             20,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        3,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-peregrine:0.1.6"
@@ -171,7 +171,7 @@ task CallWithPaftools {
         cpu_cores:          "~{num_cpus}",
         mem_gb:             20,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  3,
         max_retries:        3,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-peregrine:0.1.6"

diff --git a/wdl/deprecated/tasks/PhaseReads.wdl b/wdl/deprecated/tasks/PhaseReads.wdl
@@ -46,7 +46,7 @@ task ConvertToFastq {
         cpu_cores:          1,
         mem_gb:             4,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"
@@ -94,7 +94,7 @@ task Minimap2PAF {
         cpu_cores:          cpus,
         mem_gb:             20,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       25,
         preemptible_tries:  1,
         max_retries:        0,
         docker:             "us.gcr.io/broad-dsp-lrma/lr-align:0.1.28"