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Commit 8993b5c6 authored by Ruben Vorderman's avatar Ruben Vorderman
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Use gebibytes instead of gigabytes

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pbmm2.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -29,7 +29,7 @@ task Mapping { ...@@ -29,7 +29,7 @@ task Mapping {
File queryFile File queryFile
Int cores = 4 Int cores = 4
String memory = "30G" String memory = "30GiB"
Int timeMinutes = 1 + ceil(size(queryFile, "G") * 2000 / cores) Int timeMinutes = 1 + ceil(size(queryFile, "G") * 2000 / cores)
String dockerImage = "quay.io/biocontainers/pbmm2:1.3.0--h56fc30b_1" String dockerImage = "quay.io/biocontainers/pbmm2:1.3.0--h56fc30b_1"
} }
......
peach.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -29,7 +29,7 @@ task Peach { ...@@ -29,7 +29,7 @@ task Peach {
String outputDir = "./peach" String outputDir = "./peach"
File panelJson File panelJson
String memory = "2G" String memory = "2GiB"
String dockerImage = "quay.io/biowdl/peach:v1.5" String dockerImage = "quay.io/biowdl/peach:v1.5"
Int timeMinutes = 5 Int timeMinutes = 5
} }
......
picard.wdl
+ 30
− 30
View file @ 8993b5c6
...@@ -27,7 +27,7 @@ task BedToIntervalList { ...@@ -27,7 +27,7 @@ task BedToIntervalList {
String outputPath = "regions.interval_list" String outputPath = "regions.interval_list"
String javaXmx = "3G" String javaXmx = "3G"
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 5 Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -88,7 +88,7 @@ task CollectHsMetrics { ...@@ -88,7 +88,7 @@ task CollectHsMetrics {
Int memoryMb = javaXmxMb + 512 Int memoryMb = javaXmxMb + 512
# Additional * 2 because picard multiple metrics reads the # Additional * 2 because picard multiple metrics reads the
# reference fasta twice. # reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6) Int timeMinutes = 1 + ceil(size(referenceFasta, "GiB") * 3 * 2) + ceil(size(inputBam, "GiB") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -109,7 +109,7 @@ task CollectHsMetrics { ...@@ -109,7 +109,7 @@ task CollectHsMetrics {
} }
runtime { runtime {
memory: "~{memoryMb}M" memory: "~{memoryMb}MiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -157,7 +157,7 @@ task CollectMultipleMetrics { ...@@ -157,7 +157,7 @@ task CollectMultipleMetrics {
Int javaXmxMb = 3072 Int javaXmxMb = 3072
Int memoryMb = javaXmxMb + 512 Int memoryMb = javaXmxMb + 512
# Additional * 2 because picard multiple metrics reads the reference fasta twice. # Additional * 2 because picard multiple metrics reads the reference fasta twice.
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 3 * 2) + ceil(size(inputBam, "G") * 6) Int timeMinutes = 1 + ceil(size(referenceFasta, "GiB") * 3 * 2) + ceil(size(inputBam, "GiB") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -223,7 +223,7 @@ task CollectMultipleMetrics { ...@@ -223,7 +223,7 @@ task CollectMultipleMetrics {
} }
runtime { runtime {
memory: "~{memoryMb}M" memory: "~{memoryMb}MiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -281,9 +281,9 @@ task CollectRnaSeqMetrics { ...@@ -281,9 +281,9 @@ task CollectRnaSeqMetrics {
String strandSpecificity = "NONE" String strandSpecificity = "NONE"
String javaXmx = "8G" String javaXmx = "8G"
String memory = "9G" String memory = "9GiB"
# With 6 minutes per G there were several timeouts. # With 6 minutes per G there were several timeouts.
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 12) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 12)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -340,8 +340,8 @@ task CollectTargetedPcrMetrics { ...@@ -340,8 +340,8 @@ task CollectTargetedPcrMetrics {
String basename String basename
String javaXmx = "3G" String javaXmx = "3G"
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -402,7 +402,7 @@ task CollectVariantCallingMetrics { ...@@ -402,7 +402,7 @@ task CollectVariantCallingMetrics {
String basename String basename
String javaXmx = "8G" String javaXmx = "8G"
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 1440 Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -459,9 +459,9 @@ task CollectWgsMetrics { ...@@ -459,9 +459,9 @@ task CollectWgsMetrics {
Int? minimumBaseQuality Int? minimumBaseQuality
Int? coverageCap Int? coverageCap
String memory = "5G" String memory = "5GiB"
String javaXmx = "4G" String javaXmx = "4G"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 6) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 6)
String dockerImage = "quay.io/biocontainers/picard:2.23.2--0" String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
} }
...@@ -516,7 +516,7 @@ task CreateSequenceDictionary { ...@@ -516,7 +516,7 @@ task CreateSequenceDictionary {
String outputDir String outputDir
String javaXmx = "2G" String javaXmx = "2G"
String memory = "3G" String memory = "3GiB"
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -568,7 +568,7 @@ task GatherBamFiles { ...@@ -568,7 +568,7 @@ task GatherBamFiles {
Int javaXmxMb = 1024 Int javaXmxMb = 1024
Int memoryMb = javaXmxMb + 512 Int memoryMb = javaXmxMb + 512
# One minute per input gigabyte. # One minute per input gigabyte.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 1) Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 1)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -593,7 +593,7 @@ task GatherBamFiles { ...@@ -593,7 +593,7 @@ task GatherBamFiles {
} }
runtime { runtime {
memory: "~{memoryMb}M" memory: "~{memoryMb}MiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -630,8 +630,8 @@ task GatherVcfs { ...@@ -630,8 +630,8 @@ task GatherVcfs {
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
String javaXmx = "4G" String javaXmx = "4G"
String memory = "5G" String memory = "5GiB"
Int timeMinutes = 1 + ceil(size(inputVcfs, "G") * 2) Int timeMinutes = 1 + ceil(size(inputVcfs, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -700,7 +700,7 @@ task MarkDuplicates { ...@@ -700,7 +700,7 @@ task MarkDuplicates {
Int javaXmxMb = 6656 # 6.5G Int javaXmxMb = 6656 # 6.5G
String memoryMb = javaXmxMb + 512 String memoryMb = javaXmxMb + 512
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 8) Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 8)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -736,7 +736,7 @@ task MarkDuplicates { ...@@ -736,7 +736,7 @@ task MarkDuplicates {
} }
runtime { runtime {
memory: "~{memoryMb}M" memory: "~{memoryMb}MiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -782,8 +782,8 @@ task MergeVCFs { ...@@ -782,8 +782,8 @@ task MergeVCFs {
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
String javaXmx = "4G" String javaXmx = "4G"
String memory = "5G" String memory = "5GiB"
Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2 Int timeMinutes = 1 + ceil(size(inputVCFs, "GiB")) * 2
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -838,7 +838,7 @@ task SamToFastq { ...@@ -838,7 +838,7 @@ task SamToFastq {
Boolean paired = true Boolean paired = true
String javaXmx = "16G" # High memory default to avoid crashes. String javaXmx = "16G" # High memory default to avoid crashes.
String memory = "17G" String memory = "17GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
...@@ -900,7 +900,7 @@ task ScatterIntervalList { ...@@ -900,7 +900,7 @@ task ScatterIntervalList {
Int scatter_count Int scatter_count
String javaXmx = "3G" String javaXmx = "3G"
String memory = "4G" String memory = "4GiB"
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -943,7 +943,7 @@ task SortSam { ...@@ -943,7 +943,7 @@ task SortSam {
# 4.000000001 which gets rounded to 5. # 4.000000001 which gets rounded to 5.
# GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778 # GATK Best practices uses 75000 here: https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/d2934ed656ade44801f9cfe1c0e78d4f80684b7b/PairedEndSingleSampleWf-fc-hg38.wdl#L778
Int XmxGb = ceil(maxRecordsInRam / 125001.0) Int XmxGb = ceil(maxRecordsInRam / 125001.0)
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -971,7 +971,7 @@ task SortSam { ...@@ -971,7 +971,7 @@ task SortSam {
runtime { runtime {
cpu: 1 cpu: 1
memory: "~{1 + XmxGb}G" memory: "~{1 + XmxGb}GiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -1004,8 +1004,8 @@ task SortVcf { ...@@ -1004,8 +1004,8 @@ task SortVcf {
File? dict File? dict
String javaXmx = "8G" String javaXmx = "8G"
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5) Int timeMinutes = 1 + ceil(size(vcfFiles, "GiB") * 5)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -1054,8 +1054,8 @@ task RenameSample { ...@@ -1054,8 +1054,8 @@ task RenameSample {
String newSampleName String newSampleName
String javaXmx = "8G" String javaXmx = "8G"
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 1 + ceil(size(inputVcf, "G") * 2) Int timeMinutes = 1 + ceil(size(inputVcf, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
...@@ -1109,7 +1109,7 @@ task UmiAwareMarkDuplicatesWithMateCigar { ...@@ -1109,7 +1109,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
Boolean useJdkInflater = false Boolean useJdkInflater = false
Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater Boolean useJdkDeflater = true # Achieves much better compression rates than the intel deflater
String javaXmx = "8G" String javaXmx = "8G"
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 360 Int timeMinutes = 360
String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0" String dockerImage = "quay.io/biocontainers/picard:2.26.10--hdfd78af_0"
} }
......
prepareShiny.wdl
+ 2
− 2
View file @ 8993b5c6
...@@ -25,7 +25,7 @@ task CreateDesignMatrix { ...@@ -25,7 +25,7 @@ task CreateDesignMatrix {
File countTable File countTable
String shinyDir = "." String shinyDir = "."
String memory = "5G" String memory = "5GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0" String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
} }
...@@ -67,7 +67,7 @@ task CreateAnnotation { ...@@ -67,7 +67,7 @@ task CreateAnnotation {
File referenceGtfFile File referenceGtfFile
String shinyDir = "." String shinyDir = "."
String memory = "5G" String memory = "5GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0" String dockerImage = "quay.io/biocontainers/predex:0.9.2--pyh3252c3a_0"
} }
......
rtg.wdl
+ 4
− 4
View file @ 8993b5c6
...@@ -27,8 +27,8 @@ task Format { ...@@ -27,8 +27,8 @@ task Format {
String outputPath = "seq_data.sdf" String outputPath = "seq_data.sdf"
String rtgMem = "8G" String rtgMem = "8G"
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 1 + ceil(size(inputFiles) * 2) Int timeMinutes = 1 + ceil(size(inputFiles, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0" String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
} }
...@@ -85,8 +85,8 @@ task VcfEval { ...@@ -85,8 +85,8 @@ task VcfEval {
String rtgMem = "8G" String rtgMem = "8G"
Int threads = 1 # Tool default is number of cores in the system 😱. Int threads = 1 # Tool default is number of cores in the system 😱.
String memory = "9G" String memory = "9GiB"
Int timeMinutes = 1 + ceil(size([baseline, calls], "G") * 5) Int timeMinutes = 1 + ceil(size([baseline, calls], "GiB") * 5)
String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0" String dockerImage = "quay.io/biocontainers/rtg-tools:3.10.1--0"
} }
......
sambamba.wdl
+ 5
− 5
View file @ 8993b5c6
...@@ -27,7 +27,7 @@ task Flagstat { ...@@ -27,7 +27,7 @@ task Flagstat {
String outputPath = "./flagstat.txt" String outputPath = "./flagstat.txt"
Int threads = 2 Int threads = 2
String memory = "8G" String memory = "8GiB"
Int timeMinutes = 320 Int timeMinutes = 320
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2" String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
} }
...@@ -84,7 +84,7 @@ task Markdup { ...@@ -84,7 +84,7 @@ task Markdup {
# Added 8192 mb as a margin of safety. Real life use with this setting uses 2.7 GiB. # Added 8192 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
Int memoryMb = 8192 + sortBufferSize + 2 * ioBufferSize Int memoryMb = 8192 + sortBufferSize + 2 * ioBufferSize
# Time minute calculation does not work well for higher number of threads. # Time minute calculation does not work well for higher number of threads.
Int timeMinutes = 1 + ceil(size(inputBams, "G") * 25) / threads Int timeMinutes = 1 + ceil(size(inputBams, "GiB") * 25) / threads
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2" String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
} }
...@@ -113,7 +113,7 @@ task Markdup { ...@@ -113,7 +113,7 @@ task Markdup {
runtime { runtime {
cpu: threads cpu: threads
memory: "~{memoryMb}M" memory: "~{memoryMb}MiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -149,7 +149,7 @@ task Sort { ...@@ -149,7 +149,7 @@ task Sort {
Int memoryPerThreadGb = 4 Int memoryPerThreadGb = 4
Int threads = 1 Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb Int memoryGb = 1 + threads * memoryPerThreadGb
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2" String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
} }
...@@ -177,7 +177,7 @@ task Sort { ...@@ -177,7 +177,7 @@ task Sort {
runtime { runtime {
cpu: threads cpu: threads
memory: "~{memoryGb}G" memory: "~{memoryGb}GiB"
docker: dockerImage docker: dockerImage
time_minutes: timeMinutes time_minutes: timeMinutes
} }
......
samtools.wdl
+ 17
− 17
View file @ 8993b5c6
...@@ -26,8 +26,8 @@ task BgzipAndIndex { ...@@ -26,8 +26,8 @@ task BgzipAndIndex {
String outputDir String outputDir
String type = "vcf" String type = "vcf"
String memory = "2G" String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(inputFile, "G")) Int timeMinutes = 1 + ceil(size(inputFile, "GiB"))
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0" String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
} }
...@@ -71,7 +71,7 @@ task Faidx { ...@@ -71,7 +71,7 @@ task Faidx {
File inputFile File inputFile
String outputDir String outputDir
String memory = "2G" String memory = "2GiB"
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -119,7 +119,7 @@ task Fastq { ...@@ -119,7 +119,7 @@ task Fastq {
Int? compressionLevel Int? compressionLevel
Int threads = 1 Int threads = 1
String memory = "1G" String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(inputBam) * 2) Int timeMinutes = 1 + ceil(size(inputBam) * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -183,8 +183,8 @@ task FilterShortReadsBam { ...@@ -183,8 +183,8 @@ task FilterShortReadsBam {
File bamFile File bamFile
String outputPathBam String outputPathBam
String memory = "1G" String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 8) Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 8)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -229,7 +229,7 @@ task Flagstat { ...@@ -229,7 +229,7 @@ task Flagstat {
File inputBam File inputBam
String outputPath String outputPath
String memory = "256M" # Only 40.5 MiB used for 150G bam file. String memory = "256MiB" # Only 40.5 MiB used for 150G bam file.
Int timeMinutes = 1 + ceil(size(inputBam, "G")) Int timeMinutes = 1 + ceil(size(inputBam, "G"))
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -269,8 +269,8 @@ task Index { ...@@ -269,8 +269,8 @@ task Index {
String? outputBamPath String? outputBamPath
String memory = "2G" String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(bamFile, "G") * 4) Int timeMinutes = 1 + ceil(size(bamFile, "GiB") * 4)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -321,7 +321,7 @@ task Markdup { ...@@ -321,7 +321,7 @@ task Markdup {
File inputBam File inputBam
String outputBamPath String outputBamPath
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -359,8 +359,8 @@ task Merge { ...@@ -359,8 +359,8 @@ task Merge {
Boolean force = true Boolean force = true
Int threads = 1 Int threads = 1
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 1 + ceil(size(bamFiles, "G") * 2) Int timeMinutes = 1 + ceil(size(bamFiles, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -415,7 +415,7 @@ task Sort { ...@@ -415,7 +415,7 @@ task Sort {
Int memoryPerThreadGb = 4 Int memoryPerThreadGb = 4
Int threads = 1 Int threads = 1
Int memoryGb = 1 + threads * memoryPerThreadGb Int memoryGb = 1 + threads * memoryPerThreadGb
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 3) Int timeMinutes = 1 + ceil(size(inputBam, "GiB") * 3)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
...@@ -444,7 +444,7 @@ task Sort { ...@@ -444,7 +444,7 @@ task Sort {
runtime { runtime {
cpu: threads cpu: threads
memory: "~{memoryGb}G" memory: "~{memoryGb}GiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -473,7 +473,7 @@ task Tabix { ...@@ -473,7 +473,7 @@ task Tabix {
String outputFilePath = "indexed.vcf.gz" String outputFilePath = "indexed.vcf.gz"
String type = "vcf" String type = "vcf"
Int timeMinutes = 1 + ceil(size(inputFile, "G") * 2) Int timeMinutes = 1 + ceil(size(inputFile, "GiB") * 2)
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0" String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
} }
...@@ -526,8 +526,8 @@ task View { ...@@ -526,8 +526,8 @@ task View {
Int? MAPQthreshold Int? MAPQthreshold
Int threads = 1 Int threads = 1
String memory = "1G" String memory = "1GiB"
Int timeMinutes = 1 + ceil(size(inFile, "G") * 5) Int timeMinutes = 1 + ceil(size(inFile, "GiB") * 5)
String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0" String dockerImage = "quay.io/biocontainers/samtools:1.11--h6270b1f_0"
} }
......
scripts @ 98cc3e10
Compare 84690a30...98cc3e10
Subproject commit 84690a30eb0dde2bfdfaff9abf097b6f4c49dfd8 Subproject commit 98cc3e10125c853a70f41ceccf8f9d5428d4c1a3
smoove.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -29,7 +29,7 @@ task Call { ...@@ -29,7 +29,7 @@ task Call {
String sample String sample
String outputDir = "./smoove" String outputDir = "./smoove"
String memory = "15G" String memory = "15GiB"
Int timeMinutes = 1440 Int timeMinutes = 1440
String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0" String dockerImage = "quay.io/biocontainers/smoove:0.2.5--0"
} }
......
snpeff.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -36,7 +36,7 @@ task SnpEff { ...@@ -36,7 +36,7 @@ task SnpEff {
Boolean noShiftHgvs = false Boolean noShiftHgvs = false
Int? upDownStreamLen Int? upDownStreamLen
String memory = "9G" String memory = "9GiB"
String javaXmx = "8G" String javaXmx = "8G"
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/snpeff:5.0--0" String dockerImage = "quay.io/biocontainers/snpeff:5.0--0"
......
somaticseq.wdl
+ 5
− 5
View file @ 8993b5c6
...@@ -47,7 +47,7 @@ task ParallelPaired { ...@@ -47,7 +47,7 @@ task ParallelPaired {
File? strelkaSNV File? strelkaSNV
File? strelkaIndel File? strelkaIndel
String memory = "2G" String memory = "2GiB"
Int threads = 1 Int threads = 1
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -162,7 +162,7 @@ task ParallelPairedTrain { ...@@ -162,7 +162,7 @@ task ParallelPairedTrain {
File? strelkaSNV File? strelkaSNV
File? strelkaIndel File? strelkaIndel
String memory = "2G" String memory = "2GiB"
Int threads = 1 Int threads = 1
Int timeMinutes = 240 Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -270,7 +270,7 @@ task ParallelSingle { ...@@ -270,7 +270,7 @@ task ParallelSingle {
File? scalpelVCF File? scalpelVCF
File? strelkaVCF File? strelkaVCF
String memory = "2G" String memory = "2GiB"
Int threads = 1 Int threads = 1
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -362,7 +362,7 @@ task ParallelSingleTrain { ...@@ -362,7 +362,7 @@ task ParallelSingleTrain {
File? scalpelVCF File? scalpelVCF
File? strelkaVCF File? strelkaVCF
String memory = "2G" String memory = "2GiB"
Int threads = 1 Int threads = 1
Int timeMinutes = 240 Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -441,7 +441,7 @@ task ModifyStrelka { ...@@ -441,7 +441,7 @@ task ModifyStrelka {
File strelkaVCF File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz") String outputVCFName = basename(strelkaVCF, ".gz")
String memory = "2G" String memory = "2GiB"
Int timeMinutes = 20 Int timeMinutes = 20
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
} }
......
spades.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -100,6 +100,6 @@ task Spades { ...@@ -100,6 +100,6 @@ task Spades {
runtime { runtime {
cpu: threads cpu: threads
memory: "~{memoryGb}G" memory: "~{memoryGb}GiB"
} }
} }
star.wdl
+ 5
− 5
View file @ 8993b5c6
...@@ -29,8 +29,8 @@ task GenomeGenerate { ...@@ -29,8 +29,8 @@ task GenomeGenerate {
Int? sjdbOverhang Int? sjdbOverhang
Int threads = 4 Int threads = 4
String memory = "32G" String memory = "32GiB"
Int timeMinutes = ceil(size(referenceFasta, "G") * 240 / threads) Int timeMinutes = ceil(size(referenceFasta, "GiB") * 240 / threads)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0" String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
} }
...@@ -130,12 +130,12 @@ task Star { ...@@ -130,12 +130,12 @@ task Star {
Int runThreadN = 4 Int runThreadN = 4
String? memory String? memory
# 1 minute initialization + time reading in index (1 minute per G) + time aligning data. # 1 minute initialization + time reading in index (1 minute per G) + time aligning data.
Int timeMinutes = 1 + ceil(size(indexFiles, "G")) + ceil(size(flatten([inputR1, inputR2]), "G") * 300 / runThreadN) Int timeMinutes = 1 + ceil(size(indexFiles, "GiB")) + ceil(size(flatten([inputR1, inputR2]), "GiB") * 300 / runThreadN)
String dockerImage = "quay.io/biocontainers/star:2.7.3a--0" String dockerImage = "quay.io/biocontainers/star:2.7.3a--0"
} }
# Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index. # Use a margin of 30% index size. Real memory usage is ~30 GiB for a 27 GiB index.
Int memoryGb = 1 + ceil(size(indexFiles, "G") * 1.3) Int memoryGb = 1 + ceil(size(indexFiles, "GiB") * 1.3)
# For some reason doing above calculation inside a string does not work. # For some reason doing above calculation inside a string does not work.
# So we solve it with an optional memory string and using select_first # So we solve it with an optional memory string and using select_first
# in the runtime section. # in the runtime section.
...@@ -172,7 +172,7 @@ task Star { ...@@ -172,7 +172,7 @@ task Star {
runtime { runtime {
cpu: runThreadN cpu: runThreadN
memory: select_first([memory, "~{memoryGb}G"]) memory: select_first([memory, "~{memoryGb}GiB"])
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
......
strelka.wdl
+ 2
− 2
View file @ 8993b5c6
...@@ -63,7 +63,7 @@ task Germline { ...@@ -63,7 +63,7 @@ task Germline {
runtime { runtime {
cpu: cores cpu: cores
memory: "~{memoryGb}G" memory: "~{memoryGb}GiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -139,7 +139,7 @@ task Somatic { ...@@ -139,7 +139,7 @@ task Somatic {
runtime { runtime {
cpu: cores cpu: cores
memory: "~{memoryGb}G" memory: "~{memoryGb}GiB"
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
......
stringtie.wdl
+ 2
− 2
View file @ 8993b5c6
...@@ -34,7 +34,7 @@ task Stringtie { ...@@ -34,7 +34,7 @@ task Stringtie {
Float? minimumCoverage Float? minimumCoverage
Int threads = 1 Int threads = 1
String memory = "2G" String memory = "2GiB"
Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads) Int timeMinutes = 1 + ceil(size(bam, "G") * 60 / threads)
String dockerImage = "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0" String dockerImage = "quay.io/biocontainers/stringtie:1.3.6--h92e31bf_0"
} }
...@@ -102,7 +102,7 @@ task Merge { ...@@ -102,7 +102,7 @@ task Merge {
Float? minimumIsoformFraction Float? minimumIsoformFraction
String? label String? label
String memory = "10G" String memory = "10GiB"
Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20) Int timeMinutes = 1 + ceil(size(gtfFiles, "G") * 20)
String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0" String dockerImage = "quay.io/biocontainers/stringtie:2.1.4--h7e0af3c_0"
} }
......
survivor.wdl
+ 1
− 1
View file @ 8993b5c6
...@@ -31,7 +31,7 @@ task Merge { ...@@ -31,7 +31,7 @@ task Merge {
Int minSize = 30 Int minSize = 30
String outputPath = "./survivor/merged.vcf" String outputPath = "./survivor/merged.vcf"
String memory = "24G" String memory = "24GiB"
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0" String dockerImage = "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
} }
......
talon.wdl
+ 10
− 10
View file @ 8993b5c6
...@@ -30,7 +30,7 @@ task CreateAbundanceFileFromDatabase { ...@@ -30,7 +30,7 @@ task CreateAbundanceFileFromDatabase {
File? whitelistFile File? whitelistFile
File? datasetsFile File? datasetsFile
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -86,7 +86,7 @@ task CreateGtfFromDatabase { ...@@ -86,7 +86,7 @@ task CreateGtfFromDatabase {
File? whitelistFile File? whitelistFile
File? datasetFile File? datasetFile
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -144,7 +144,7 @@ task FilterTalonTranscripts { ...@@ -144,7 +144,7 @@ task FilterTalonTranscripts {
File? datasetsFile File? datasetsFile
Int? minDatasets Int? minDatasets
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -200,7 +200,7 @@ task GetReadAnnotations { ...@@ -200,7 +200,7 @@ task GetReadAnnotations {
File? datasetFile File? datasetFile
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -248,7 +248,7 @@ task GetSpliceJunctions { ...@@ -248,7 +248,7 @@ task GetSpliceJunctions {
String runMode = "intron" String runMode = "intron"
String outputPrefix String outputPrefix
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -302,7 +302,7 @@ task InitializeTalonDatabase { ...@@ -302,7 +302,7 @@ task InitializeTalonDatabase {
Int cutOff3p = 300 Int cutOff3p = 300
String outputPrefix String outputPrefix
String memory = "10G" String memory = "10GiB"
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -360,7 +360,7 @@ task LabelReads { ...@@ -360,7 +360,7 @@ task LabelReads {
String outputPrefix String outputPrefix
Int threads = 4 Int threads = 4
String memory = "25G" String memory = "25GiB"
Int timeMinutes = 2880 Int timeMinutes = 2880
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -413,7 +413,7 @@ task ReformatGtf { ...@@ -413,7 +413,7 @@ task ReformatGtf {
input { input {
File gtfFile File gtfFile
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -454,7 +454,7 @@ task SummarizeDatasets { ...@@ -454,7 +454,7 @@ task SummarizeDatasets {
File? datasetGroupsCsv File? datasetGroupsCsv
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 50 Int timeMinutes = 50
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
...@@ -506,7 +506,7 @@ task Talon { ...@@ -506,7 +506,7 @@ task Talon {
String outputPrefix String outputPrefix
Int threads = 4 Int threads = 4
String memory = "25G" String memory = "25GiB"
Int timeMinutes = 2880 Int timeMinutes = 2880
String dockerImage = "biocontainers/talon:v5.0_cv1" String dockerImage = "biocontainers/talon:v5.0_cv1"
} }
......
transcriptclean.wdl
+ 3
− 3
View file @ 8993b5c6
...@@ -27,7 +27,7 @@ task GetSJsFromGtf { ...@@ -27,7 +27,7 @@ task GetSJsFromGtf {
String outputPrefix String outputPrefix
Int minIntronSize = 21 Int minIntronSize = 21
String memory = "8G" String memory = "8GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1" String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
} }
...@@ -72,7 +72,7 @@ task GetTranscriptCleanStats { ...@@ -72,7 +72,7 @@ task GetTranscriptCleanStats {
File inputSam File inputSam
String outputPrefix String outputPrefix
String memory = "4G" String memory = "4GiB"
Int timeMinutes = 30 Int timeMinutes = 30
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1" String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
} }
...@@ -128,7 +128,7 @@ task TranscriptClean { ...@@ -128,7 +128,7 @@ task TranscriptClean {
File? variantFile File? variantFile
Int cores = 1 Int cores = 1
String memory = "25G" String memory = "25GiB"
Int timeMinutes = 2880 Int timeMinutes = 2880
String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1" String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
} }
......
umi-tools.wdl
+ 3
− 3
View file @ 8993b5c6
...@@ -30,7 +30,7 @@ task Extract { ...@@ -30,7 +30,7 @@ task Extract {
String? read2Output = "umi_extracted_R2.fastq.gz" String? read2Output = "umi_extracted_R2.fastq.gz"
Boolean threePrime = false Boolean threePrime = false
String memory = "20G" String memory = "20GiB"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2) Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0" String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
} }
...@@ -87,8 +87,8 @@ task Dedup { ...@@ -87,8 +87,8 @@ task Dedup {
String? umiSeparator String? umiSeparator
String? statsPrefix String? statsPrefix
String memory = "25G" String memory = "25GiB"
Int timeMinutes = 30 + ceil(size(inputBam, "G") * 30) Int timeMinutes = 30 + ceil(size(inputBam, "GiB") * 30)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0" String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
} }
......
umi.wdl
+ 2
− 2
View file @ 8993b5c6
...@@ -30,8 +30,8 @@ task BamReadNameToUmiTag { ...@@ -30,8 +30,8 @@ task BamReadNameToUmiTag {
String outputPath = "output.bam" String outputPath = "output.bam"
String umiTag = "RX" String umiTag = "RX"
String memory = "2G" String memory = "2GiB"
Int timeMinutes = 1 + ceil(size([inputBam], "G") * 10) Int timeMinutes = 1 + ceil(size([inputBam], "GiB") * 10)
String dockerImage = "quay.io/biocontainers/pysam:0.17.0--py39h051187c_0" String dockerImage = "quay.io/biocontainers/pysam:0.17.0--py39h051187c_0"
} }
......
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