Merge pull request #126 from biowdl/BIOWDL-282

Regions no longer required for several GATK tasks

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ 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 {
@@ -299,7 +299,7 @@ task SplitNCigarReads {
         File referenceFastaDict
         File referenceFastaFai
         String outputBam
-        Array[File]+ intervals
+        Array[File] intervals = []
 
         Int memory = 4
         Float memoryMultiplier = 4
@@ -314,7 +314,7 @@ task SplitNCigarReads {
         -I ~{inputBam} \
         -R ~{referenceFasta} \
         -O ~{outputBam} \
-        -L ~{sep=' -L ' intervals}
+        ~{true="-L" false="" length(intervals) > 0} ~{sep=' -L ' intervals}
     }
 
     output {