small adjustments

bwa.wdl

@@ -28,6 +28,7 @@ task Mem {
         String outputPrefix
         Boolean sixtyFour = false
         Boolean usePostalt = false
+        Boolean useSoftclippingForSupplementary = false
         Int sortMemoryPerThreadGb = 2
         Int compressionLevel = 1
 
@@ -36,7 +37,7 @@ task Mem {
 
         Int threads = 4
         Int? memoryGb
-        Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 260 / threads)
+        Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 500 / threads)
         # Contains bwa 0.7.17 bwakit 0.7.17.dev1 and samtools 1.10.
         String dockerImage = "quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0"
     }
@@ -56,6 +57,7 @@ task Mem {
         mkdir -p "$(dirname ~{outputPrefix})"
         bwa mem \
           -t ~{threads} \
+          ~{if useSoftclippingForSupplementary then "-Y" else ""} \
           ~{"-R '" + readgroup}~{true="'" false="" defined(readgroup)} \
           ~{bwaIndex.fastaFile} \
           ~{read1} \

gridss.wdl

@@ -35,9 +35,9 @@ task GRIDSS {
         String? normalLabel
 
         Int jvmHeapSizeGb = 30
-        Int threads = 2
-        Int timeMinutes = ceil(2880 / threads) + 10
-        String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0"
+        Int threads = 4
+        Int timeMinutes = ceil(5760 / threads) + 10
+        String dockerImage = "quay.io/biocontainers/gridss:2.9.3--0"
     }
 
     command {

hmftools.wdl

@@ -181,13 +181,13 @@ task GripssApplicationKt {
 
         String memory = "25G"
         String javaXmx = "24G"
-        Int timeMinutes = 60
-        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+        Int timeMinutes = 120
+        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.7--0"
     }
 
     command {
         java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+        -cp /usr/local/share/hmftools-gripss-1.7-0/gripss.jar \
         com.hartwig.hmftools.gripss.GripssApplicationKt \
         -ref_genome ~{referenceFasta} \
         -breakpoint_hotspot ~{breakpointHotspot} \
@@ -234,13 +234,13 @@ task GripssHardFilterApplicationKt {
 
         String memory = "25G"
         String javaXmx = "24G"
-        Int timeMinutes = 60
-        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.8--0"
+        Int timeMinutes = 120
+        String dockerImage = "quay.io/biocontainers/hmftools-gripss:1.7--0"
     }
 
     command {
         java -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
-        -cp /usr/local/share/hmftools-gripss-1.8-0/gripss.jar \
+        -cp /usr/local/share/hmftools-gripss-1.7-0/gripss.jar \
         com.hartwig.hmftools.gripss.GripssHardFilterApplicationKt \
         -input_vcf ~{inputVcf} \
         -output_vcf ~{outputPath} 

sambamba.wdl

@@ -84,7 +84,7 @@ task Markdup {
         # Added 1024 mb as a margin of safety. Real life use with this setting uses 2.7 GiB.
         Int memoryMb = 1024 + sortBufferSize + 2 * ioBufferSize
         # Time minute calculation does not work well for higher number of threads.
-        Int timeMinutes = 1 + ceil(size(inputBams, "G") * 16) / threads
+        Int timeMinutes = 1 + ceil(size(inputBams, "G") * 32) / threads
         String dockerImage = "quay.io/biocontainers/sambamba:0.7.1--h148d290_2"
     }