update scripts and changelog

CHANGELOG.md

@@ -9,6 +9,43 @@ that users understand how the changes affect the new version.
 -->
 version 5.1.0-dev
 ---------------------------
++ Added a task for SnpEff.
++ Adjusted runtime settings for sambamba Markdup.
++ Added a task for sambamba Flagstat.
++ Added a task for Picard CollectWgsMetrics.
++ Added a task for Peach.
++ Added tasks for HMFtools:
+  + Amber
+  + Cobalt
+  + Cuppa
+  + CuppaChart
+  + GripssApplicationKt
+  + GripssHardFilterApplicationKt
+  + HealthChecker
+  + Linx
+  + Protect
+  + Purple
+  + Sage
+  + VirusInterpreter
++ Added a task for VirusBreakend.
++ Added a task for GridssAnnotateVcfRepeatmasker. 
++ Bumped GRIDSS version to 2.12.2.
++ Adjusted GRIDSS runtime settings.
++ Added optional inputs to GRIDSS:
+  + blacklistBed
+  + gridssProperties
++ Added a task for GRIDSS AnnotateInsertedSequence.
++ Added a task for ExtractSigPredictHRD.
++ Added a task for DeconstructSigs.
++ Added option useSoftclippingForSupplementary (default false) to
+  BWA mem.
++ Adjusted BWA mem runtime settings.
++ Added a task for bedtools coverage.
++ Added a task for bcftools filter.
++ Adjusted runtime settings for bcftools annotate.
++ Added optional inputs to bcftools annotate:
+  + inputFileIndex
+  + annsFileIndex
 + Update parameter_meta for macs2
 + Add sample position in array task.
 

bcftools.wdl

@@ -44,8 +44,8 @@ task Annotate {
         String? regions
         File? regionsFile
         File? renameChrs
-        File? samplesFile        
-        
+        File? samplesFile
+
         Int threads = 0
         String memory = "4G"
         Int timeMinutes = 60 + ceil(size(inputFile, "G"))

scripts @ 84690a30

-Subproject commit c31670d3a9222a2feafc649cbc118c95afbc7189
+Subproject commit 84690a30eb0dde2bfdfaff9abf097b6f4c49dfd8