diff --git a/CHANGELOG.md b/CHANGELOG.md index 28e998e6887623a28c519dc59c5c34300a54447f..e47033c6ba7e793110c9a940e081718a7acf4840 100644 --- a/CHANGELOG.md +++ b/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) diff --git a/CPAT.wdl b/CPAT.wdl index afb6785392f7b71aa57f32ada4f31db3e4efc138..4a6d44786a70570fdcdefe0228242e61c6d1fd22 100644 --- a/CPAT.wdl +++ b/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"} diff --git a/gffcompare.wdl b/gffcompare.wdl index 5c83ba9d9a0bc790d53b74fc0391e86b294e2dff..aa7c720916c9f1895197a3c36975c2f326266e20 100644 --- a/gffcompare.wdl +++ b/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"} diff --git a/gffread.wdl b/gffread.wdl index 967dd5c9afea4d200a63ad101ec06957c4fa6cc9..a04540f531de2f4375de76a22bbf55708698857b 100644 --- a/gffread.wdl +++ b/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"}