time_minutes

ccs.wdl

@@ -33,6 +33,7 @@ task CCS {
         
         Int cores = 2
         String memory = "2G"
+        Int timeMinutes = 120
         String dockerImage = "quay.io/biocontainers/pbccs:4.2.0--0"
     }
 
@@ -63,6 +64,7 @@ task CCS {
     runtime {
         cpu: cores
         memory: memory
+        time_minutes: timeMinutes
         docker: dockerImage
     }
 
@@ -78,6 +80,7 @@ task CCS {
         outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
         cores: {description: "The number of cores to be used.", 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"}
 
         # outputs

isoseq3.wdl

@@ -32,6 +32,7 @@ task Refine {
 
         Int cores = 2
         String memory = "2G"
+        Int timeMinutes = 180
         String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
     }
 
@@ -61,6 +62,7 @@ task Refine {
     runtime {
         cpu: cores
         memory: memory
+        time_minutes: timeMinutes
         docker: dockerImage
     }
 
@@ -75,6 +77,7 @@ task Refine {
         outputNamePrefix: {description: "Basename of the output files.", category: "required"}
         cores: {description: "The number of cores to be used.", 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"}
 
         # outputs

lima.wdl

@@ -50,6 +50,7 @@ task Lima {
         
         Int cores = 2
         String memory = "2G"
+        Int timeMinutes = 1440
         String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
     }
 
@@ -110,6 +111,7 @@ task Lima {
     runtime {
         cpu: cores
         memory: memory
+        time_minutes: timeMinutes
         docker: dockerImage
     }
 
@@ -142,6 +144,7 @@ task Lima {
         outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
         cores: {description: "The number of cores to be used.", 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"}
 
         # outputs

talon.wdl

@@ -31,7 +31,7 @@ task CreateAbundanceFileFromDatabase {
         File? datasetsFile
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -87,7 +87,7 @@ task CreateGtfFromDatabase {
         File? datasetFile
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -141,7 +141,7 @@ task FilterTalonTranscripts {
         File? pairingsFile
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -189,7 +189,7 @@ task GetReadAnnotations {
         File? datasetFile
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -240,7 +240,7 @@ task InitializeTalonDatabase {
         String outputPrefix
 
         String memory = "10G"
-        Int timeMinutes = 1
+        Int timeMinutes = 60
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -292,7 +292,7 @@ task ReformatGtf {
         File GTFfile
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 
@@ -333,7 +333,7 @@ task SummarizeDatasets {
         File? datasetGroupsCSV
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 50
         String dockerImage = "biocontainers/talon:v4.4.2_cv1"
     }
 

transcriptclean.wdl

@@ -28,7 +28,7 @@ task GetSJsFromGtf {
         Int minIntronSize = 21
 
         String memory = "8G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
     }
 
@@ -73,7 +73,7 @@ task GetTranscriptCleanStats {
         String outputPrefix
 
         String memory = "4G"
-        Int timeMinutes = 1
+        Int timeMinutes = 30
         String dockerImage = "biocontainers/transcriptclean:v2.0.2_cv1"
     }