Fix memory values.

CHANGELOG.md

@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 
 version 5.0.0-dev
 ---------------------------
++ Add memory values to GffCompare, GffRead and CPAT.
 + GffCompare: Make the `referenceAnnotation` input optional.
 + Stringtie: Add the `minimumCoverage` input.
 + UMI-tools: update default dockerImage to use umitools v1.1.1 with correct samtools version (1.10)

CPAT.wdl

@@ -34,6 +34,7 @@ task CPAT {
         Array[String]? startCodons
         Array[String]? stopCodons
 
+        String memory = "4G"
         Int timeMinutes = 10 + ceil(size(gene, "G") * 30)
         String dockerImage = "biocontainers/cpat:v1.2.4_cv1"
     }
@@ -60,8 +61,9 @@ task CPAT {
     }
 
     runtime {
-        docker: dockerImage
+        memory: memory
         time_minutes: timeMinutes
+        docker: dockerImage
     }
 
     parameter_meta {
@@ -74,6 +76,7 @@ task CPAT {
         referenceGenomeIndex: {description: "The index of the reference. Should be added as input if CPAT should not index the reference genome.", category: "advanced"}
         startCodons: {description: "Equivalent to CPAT's `--start` option.", category: "advanced"}
         stopCodons: {description: "Equivalent to CPAT's `--stop` option.", category: "advanced"}
+        memory: {description: "The amount of memory available to the job.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
 

gffcompare.wdl

@@ -46,6 +46,7 @@ task GffCompare {
         Int? maxDistanceGroupingTranscriptStartSites
         String? namePrefix
 
+        String memory = "4G"
         Int timeMinutes = 1 + ceil(size(inputGtfFiles, "G") * 30)
         String dockerImage = "quay.io/biocontainers/gffcompare:0.10.6--h2d50403_0"
 
@@ -114,6 +115,7 @@ task GffCompare {
     }
 
     runtime {
+        memory: memory
        time_minutes: timeMinutes
        docker: dockerImage
     }
@@ -140,6 +142,7 @@ task GffCompare {
         maxDistanceFreeEndsTerminalExons: {description: "Equivalent to gffcompare's `-e` option.", category: "advanced"}
         maxDistanceGroupingTranscriptStartSites: {description: "Equivalent to gffcompare's `-d` option.", category: "advanced"}
         namePrefix: {description: "Equivalent to gffcompare's `-p` option.", category: "advanced"}
+        memory: {description: "The amount of memory available to the job.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
 

gffread.wdl

@@ -32,6 +32,7 @@ task GffRead {
         String? proteinFastaPath
         String? filteredGffPath
 
+        String memory = "4G"
         Int timeMinutes = 1 + ceil(size(inputGff, "G") * 10)
         String dockerImage = "quay.io/biocontainers/gffread:0.9.12--0"
     }
@@ -64,6 +65,7 @@ task GffRead {
     }
 
     runtime {
+        memory: memory
         time_minutes: timeMinutes
         docker: dockerImage
     }
@@ -78,6 +80,7 @@ task GffRead {
         CDSFastaPath: {description: "The location the CDS fasta should be written to.", category: "advanced"}
         proteinFastaPath: {description: "The location the protein fasta should be written to.", category: "advanced"}
         filteredGffPath: {description: "The location the filtered GFF should be written to.", category: "advanced"}
+        memory: {description: "The amount of memory available to the job.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}