Update runtime.

CHANGELOG.md

@@ -10,6 +10,7 @@ that users understand how the changes affect the new version.
 -->
 version 3.1.0
 ---------------------------
++ Add time_minutes runtime to CCS, Lima & IsoSeq3.
 + Lima: Replace mv command with cp.
 + Default threads for BWA in bwa.Kit task: 4. Samtools sort in the
   same task: 1. Output BAM compression level to 1.

ccs.wdl

@@ -34,6 +34,7 @@ task CCS {
         Int cores = 4
         String memory = "10G"
         String dockerImage = "quay.io/biocontainers/pbccs:4.2.0--0"
+        Int timeMinutes = ceil(size(subreadsFile, "G") * 240 / cores)
     }
 
     command {
@@ -64,6 +65,7 @@ task CCS {
         cpu: cores
         memory: memory
         docker: dockerImage
+        time_minutes: timeMinutes
     }
 
     parameter_meta {

isoseq3.wdl

@@ -32,6 +32,7 @@ task Refine {
         Int cores = 4
         String memory = "10G"
         String dockerImage = "quay.io/biocontainers/isoseq3:3.3.0--0"
+        Int timeMinutes = ceil(size(inputBamFile, "G") * 240 / cores)
     }
 
     command <<<
@@ -77,6 +78,7 @@ task Refine {
         cpu: cores
         memory: memory
         docker: dockerImage
+        time_minutes: timeMinutes
     }
 
     parameter_meta {

lima.wdl

@@ -51,6 +51,7 @@ task Lima {
         Int cores = 4
         String memory = "10G"
         String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
+        Int timeMinutes = ceil(size(inputBamFile, "G") * 240 / cores)
     }
 
     Map[String, String] libraryDesignOptions = {"same": "--same", "different": "--different", "neighbors": "--neighbors"}
@@ -111,6 +112,7 @@ task Lima {
         cpu: cores
         memory: memory
         docker: dockerImage
+        time_minutes: timeMinutes
     }
 
     parameter_meta {