Merge remote-tracking branch 'origin/develop' into gridss

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 4.0.0-develop
 ---------------------------
++ Picard MergeVcf now uses compression level 1 by default.
 + bwa mem, bwa mem+kit and hisat2 have their samtools sort threads tweaked. The
   number of threads is now related to the number of threads on the aligner.
   Using more threads reduces the chance of the samtools sort pipe getting 

cutadapt.wdl

@@ -81,7 +81,7 @@ task Cutadapt {
         Int cores = 4
         String memory = "~{300 + 100 * cores}M"
         Int timeMinutes = 1 + ceil(size([read1, read2], "G")  * 12.0 / cores)
-        String dockerImage = "quay.io/biocontainers/cutadapt:2.10--py37h516909a_0"
+        String dockerImage = "quay.io/biocontainers/cutadapt:2.10--py37hf01694f_1"
     }
 
     String realRead2output = select_first([read2output, "cut_r2.fq.gz"])

picard.wdl

@@ -553,8 +553,14 @@ task MergeVCFs {
 
         String memory = "5G"
         String javaXmx = "4G"
-        Int timeMinutes = 1 + ceil(size(inputVCFs, "G"))
+        Int timeMinutes = 1 + ceil(size(inputVCFs, "G")) * 2
         String dockerImage = "quay.io/biocontainers/picard:2.23.2--0"
+        Int compressionLevel = 1
+        Boolean useJdkInflater = true  # Slightly faster than the intel one. 
+        # Better results for compression level 1 (much smaller). Higher compression levels similar to intel deflater.
+        # NOTE: this might change in the future when the intel deflater is updated!
+        Boolean useJdkDeflater = true
+
     }
 
     # Using MergeVcfs instead of GatherVcfs so we can create indices
@@ -566,7 +572,10 @@ task MergeVCFs {
         picard -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
         MergeVcfs \
         INPUT=~{sep=' INPUT=' inputVCFs} \
-        OUTPUT=~{outputVcfPath}
+        OUTPUT=~{outputVcfPath} \
+        COMPRESSION_LEVEL=~{compressionLevel} \
+        USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
+        USE_JDK_DEFLATER=~{true="true" false="false" useJdkDeflater}   
     }
 
     output {
@@ -592,6 +601,9 @@ task MergeVCFs {
         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"}
+        useJdkInflater: {description: "True, uses the java inflater. False, uses the optimized intel inflater.", category: "advanced"}
+        useJdkDeflater: {description: "True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.", category: "advanced"}
+        compressionLevel: {description: "The compression level at which the BAM files are written", category: "advanced"}
     }
 }