Update lima to match isoseq3 and ccs changes.

CHANGELOG.md

@@ -19,6 +19,7 @@ version 5.0.0-dev
 + Bwa & bwa-mem2: Add parameter_meta for `outputHla`.
 + Multiqc: Removed WDL_AID excludes of "finished" & "dependencies" inputs.
 + Bam2fastx: Add localisation of input files to Bam2Fasta task.
++ Lima: `cores` input has been renamed to `threads` to match tool naming.
 + isoseq3: `cores` input has been renamed to `threads` to match tool naming.
 + CCS: `cores` input has been renamed to `threads` to match tool naming.
 + Add PacBio preprocessing specific tasks `mergePacBio` & `ccsChunks`.

lima.wdl

@@ -48,7 +48,7 @@ task Lima {
         File barcodeFile
         String outputPrefix
         
-        Int cores = 2
+        Int threads = 2
         String memory = "2G"
         Int timeMinutes = 30
         String dockerImage = "quay.io/biocontainers/lima:1.11.0--0"
@@ -82,7 +82,7 @@ task Lima {
         --guess-min-count ~{guessMinCount} \
         ~{true="--peek-guess" false="" peekGuess} \
         --log-level ~{logLevel} \
-        --num-threads ~{cores} \
+        --num-threads ~{threads} \
         ~{"--log-file " + outputPrefix + ".stderr.log"} \
         ~{inputBamFile} \
         ~{barcodeFile} \
@@ -110,7 +110,7 @@ task Lima {
     }
 
     runtime {
-        cpu: cores
+        cpu: threads
         memory: memory
         time_minutes: timeMinutes
         docker: dockerImage
@@ -143,7 +143,7 @@ task Lima {
         inputBamFile: {description: "Bam input file.", category: "required"}
         barcodeFile: {description: "Barcode/primer fasta file.", category: "required"}
         outputPrefix: {description: "Output directory path + output file prefix.", category: "required"}
-        cores: {description: "The number of cores to be used.", category: "advanced"}
+        threads: {description: "The number of threads 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"}