Merge branch 'm2-gatk4.1.2.0-updates' of https://github.com/Amfgcp/tasks into...

Merge branch 'm2-gatk4.1.2.0-updates' of https://github.com/Amfgcp/tasks into m2-gatk4.1.2.0-updates

CHANGELOG.md

@@ -15,6 +15,8 @@ version 1.0.0-dev
 + Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
 + Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0. 
 + Mutect2: Add necessary missing index attribute for panel of normals.
++ MultiQC: Add memory variable to multiqc task.
++ GATK: SplitNCigarReads, BaseRecalibration and ApplyBQSR do no longer need regions files as required inputs.
 + VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
 + Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
 + Cutadapt: Fix issues with read2output when using single-end reads.

gatk.wdl

@@ -7,7 +7,7 @@ task ApplyBQSR {
         File inputBamIndex
         String outputBamPath
         File recalibrationReport
-        Array[File]+ sequenceGroupInterval
+        Array[File] sequenceGroupInterval = []
         File referenceFasta
         File referenceFastaDict
         File referenceFastaFai
@@ -32,7 +32,7 @@ task ApplyBQSR {
         --static-quantized-quals 10 \
         --static-quantized-quals 20 \
         --static-quantized-quals 30 \
-        -L ~{sep=" -L " sequenceGroupInterval}
+        ~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
     }
 
     output {
@@ -53,7 +53,7 @@ task BaseRecalibrator {
         File inputBam
         File inputBamIndex
         String recalibrationReportPath
-        Array[File]+ sequenceGroupInterval
+        Array[File] sequenceGroupInterval = []
         Array[File]? knownIndelsSitesVCFs
         Array[File]? knownIndelsSitesVCFIndexes
         File? dbsnpVCF
@@ -82,7 +82,7 @@ task BaseRecalibrator {
         --use-original-qualities \
         -O ~{recalibrationReportPath} \
         --known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
-        -L ~{sep=" -L " sequenceGroupInterval}
+        ~{true="-L" false="" length(sequenceGroupInterval) > 0} ~{sep=' -L ' sequenceGroupInterval}
     }
 
     output {
@@ -478,7 +478,7 @@ task SplitNCigarReads {
         File referenceFastaDict
         File referenceFastaFai
         String outputBam
-        Array[File]+ intervals
+        Array[File] intervals = []
 
         Int memory = 4
         Float memoryMultiplier = 4
@@ -493,7 +493,7 @@ task SplitNCigarReads {
         -I ~{inputBam} \
         -R ~{referenceFasta} \
         -O ~{outputBam} \
-        -L ~{sep=' -L ' intervals}
+        ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
     }
 
     output {

multiqc.wdl

@@ -38,6 +38,7 @@ task MultiQC {
         Boolean verbose  = false
         Boolean quiet = false
         Array[Boolean] finished = []  # An array of booleans that can be used to let multiqc wait on stuff.
+        Int memory = 4
     }
 
     command {
@@ -86,6 +87,7 @@ task MultiQC {
     }
 
     runtime {
+        memory: memory
         docker: dockerImage
     }
 }