diff --git a/biopet/bamstats.wdl b/biopet/bamstats.wdl index d5a30f055c12ff13aca71b91a999c1f9c5b299ae..a00ed97efb18dbea04c842e9e05ec51c135558f8 100644 --- a/biopet/bamstats.wdl +++ b/biopet/bamstats.wdl @@ -16,15 +16,15 @@ task Generate { String outputDir Reference? reference - Int memory = 8 - Float memoryMultiplier = 2.0 + String memory = "16G" + String javaXmx = "8G" } File referenceFasta = if defined(reference) then select_first([reference]).fasta else "" String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " + toolJar - else "biopet-bamstats -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-bamstats -Xmx~{javaXmx}" command { set -e -o pipefail @@ -46,6 +46,6 @@ task Generate { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } \ No newline at end of file diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl index 92f38eff29434d7e41ef87d428e1187025dd4ae6..8cf23813bd0880c726010316c02d802b8eef922a 100644 --- a/biopet/biopet.wdl +++ b/biopet/biopet.wdl @@ -11,13 +11,13 @@ task BaseCounter { String outputDir String prefix - Int memory = 4 - Float memoryMultiplier = 3.5 + String memory = "14G" + String javaXmx = "4G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " +toolJar - else "biopet-basecounter -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-basecounter -Xmx~{javaXmx}" command { set -e -o pipefail @@ -68,7 +68,7 @@ task BaseCounter { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } @@ -155,13 +155,13 @@ task FastqSync { String out2path File? toolJar - Int memory = 4 - Float memoryMultiplier = 2.5 + String memory = "10G" + String javaXmx = "4G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " +toolJar - else "biopet-fastqsync -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-fastqsync -Xmx~{javaXmx}" command { set -e -o pipefail @@ -184,7 +184,7 @@ task FastqSync { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl index 321b77c78759da1a1c8c17f6582ab497fc04de28..59f0bad26b971fa7c3ccd9819756158621be3083 100644 --- a/biopet/sampleconfig.wdl +++ b/biopet/sampleconfig.wdl @@ -14,13 +14,13 @@ task SampleConfig { String? jsonOutputPath String? tsvOutputPath - Int memory = 4 - Float memoryMultiplier = 2.0 + String memory = "8G" + String javaXmx = "16G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " +toolJar - else "biopet-sampleconfig -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-sampleconfig -Xmx~{javaXmx}" command { set -e -o pipefail @@ -43,7 +43,7 @@ task SampleConfig { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } @@ -54,13 +54,13 @@ task SampleConfigCromwellArrays { Array[File]+ inputFiles String outputPath - Int memory = 4 - Float memoryMultiplier = 2.0 + String memory = "8G" + String javaXmx = "4G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " + toolJar - else "biopet-sampleconfig -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-sampleconfig -Xmx~{javaXmx}" command { set -e -o pipefail @@ -76,7 +76,7 @@ task SampleConfigCromwellArrays { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } @@ -90,13 +90,13 @@ task CaseControl { String outputPath String controlTag = "control" - Int memory = 4 - Float memoryMultiplier = 2.0 + String memory = "8G" + String javaXmx = "4G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " + toolJar - else "biopet-sampleconfig -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-sampleconfig -Xmx~{javaXmx}" command { set -e -o pipefail @@ -115,6 +115,6 @@ task CaseControl { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl index c8b591f79bda4559bee8abf540acea2029eae458..ade4b45da4b8c0f2af7b2fa3881a0a652e77f7aa 100644 --- a/biopet/seqstat.wdl +++ b/biopet/seqstat.wdl @@ -14,13 +14,13 @@ task Generate { String library String readgroup - Int memory = 4 - Float memoryMultiplier = 2.5 + String memory = "10G" + String javaXmx = "4G" } String toolCommand = if defined(toolJar) - then "java -Xmx" + memory + "G -jar " + toolJar - else "biopet-seqstat -Xmx" + memory + "G" + then "java -Xmx~{javaXmx} -jar " + toolJar + else "biopet-seqstat -Xmx~{javaXmx}" command { set -e -o pipefail @@ -40,6 +40,6 @@ task Generate { } runtime { - memory: ceil(memory * memoryMultiplier) + memory: memory } } \ No newline at end of file diff --git a/centrifuge.wdl b/centrifuge.wdl index ac8cd5a296e4e907a6aac4de9b73ca96f41ebabd..ec6652f93de5f29c1338f7d7ee7d7f3e9192d0f0 100644 --- a/centrifuge.wdl +++ b/centrifuge.wdl @@ -27,7 +27,7 @@ task Build { Int? kmerCount Int threads = 8 - Int memory = 20 + String memory = "20G" } command { @@ -81,7 +81,7 @@ task Classify { Array[String]? excludeTaxIds Int threads = 4 - Int memory = 8 + String memory = "8G" } String outputFilePath = outputDir + "/centrifuge.out" @@ -205,7 +205,7 @@ task Kreport { Int? minLength Int cores = 1 - Int memory = 4 + String memory = "4G" } String kreportFilePath = outputDir + "/" + prefix + "." + suffix diff --git a/collect-columns.wdl b/collect-columns.wdl index 57d246718272c21f373b20abf5cc95160f832877..fce0cfa9a9ebdb8232057222858e589be607e521 100644 --- a/collect-columns.wdl +++ b/collect-columns.wdl @@ -36,10 +36,10 @@ task CollectColumns { File outputTable = outputPath } - Int memoryGigs = 4 + ceil(0.5 * length(inputTables)) + Int memoryGb = 4 + ceil(0.5 * length(inputTables)) runtime { - memory: "~{memoryGigs}G" + memory: "~{memoryGb}G" docker: dockerImage } } \ No newline at end of file diff --git a/flash.wdl b/flash.wdl index 81703604308ba8b8252ab817aa2d010892384698..03a3646c468ba3aa31e9468aa2639a1ff6acad36 100644 --- a/flash.wdl +++ b/flash.wdl @@ -13,7 +13,7 @@ task Flash { Boolean compress = true Int threads = 2 - Int memory = 2 + String memory = "2G" } command { diff --git a/stringtie.wdl b/stringtie.wdl index d9b7cdcc1a21ebaa63e4c43f93ee630c44962772..dd267aa5b63236b2328a29b3f1863191ef8b680a 100644 --- a/stringtie.wdl +++ b/stringtie.wdl @@ -55,7 +55,7 @@ task Merge { Boolean keepMergedTranscriptsWithRetainedIntrons = false String? label - Int memory = 10 + String memory = "10G" String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0" }