Remove additional thread nonsense

bwa.wdl

@@ -92,16 +92,13 @@ task Kit {
         Boolean sixtyFour = false
 
         Int threads = 4
-
-        # Samtools uses *additional* threads. So by default this option should
-        # not be used.
-        Int sortThreads = 0
+        Int sortThreads = 1
         # Compression uses zlib. Higher than level 2 causes enormous slowdowns.
         # GATK/Picard default is level 2.
         Int sortMemoryPerThreadGb = 4
         Int compressionLevel = 1
         # BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
-        Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * (sortThreads + 1)
+        Int memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") * 1.2) + sortMemoryPerThreadGb * sortThreads
         Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
         String dockerImage = "biowdl/bwakit:0.7.17-dev-experimental"
     }
@@ -152,7 +149,7 @@ task Kit {
         sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
         threads: {description: "The number of threads to use for alignment.", category: "advanced"}
         memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
-        sortThreads: {description: "The number of additional threads to use for sorting.", category: "advanced"}
+        sortThreads: {description: "The number of threads to use for sorting.", category: "advanced"}
         sortMemoryPerThreadGb: {description: "The amount of memory for each sorting thread in gigabytes.", category: "advanced"}
         compressionLevel: {description: "The compression level of the output BAM.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}

sambamba.wdl

@@ -25,7 +25,6 @@ task Markdup {
     input {
         Array[File] inputBams
         String outputPath
-        # Sambamba additional threads like samtools
         Int threads = 1
         Int compressionLevel = 1
         Int? hashTableSize
@@ -76,7 +75,6 @@ task Sort {
         String outputPath = basename(inputBam, "\.bam") + ".sorted.bam"
         Boolean sortByName = false
         Int compressionLevel = 1
-        # Sambamba additional threads like samtools
         Int threads = 1
         Int memoryPerThreadGb = 4
         Int memoryGb = 1 + threads * memoryPerThreadGb
@@ -122,7 +120,7 @@ task Sort {
         memoryGb: {description: "The amount of memory available to the job in gigabytes.", category: "advanced"}
         memoryPerThreadGb: {description: "The amount of memory used per sort thread in gigabytes", 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"}
-        threads: {description: "The number of additional threads that will be used for this task.", category: "advanced"}
+        threads: {description: "The number of threads that will be used for this task.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
         # outputs
         outputBam: {description: "Sorted BAM file."}