expose --skipMarkDupes and --plotOnlyNonDuplicates in WDL (#925)

expose --skipMarkDupes and --plotOnlyNonDuplicates in WDL task plot_coverage in tasks_reports.wdl

pipes/WDL/workflows/tasks/tasks_reports.wdl

@@ -13,6 +13,9 @@ task plot_coverage {
  String? aligner="novoalign" # novoalign or bwa
  String? aligner_options="-r Random -l 40 -g 40 -x 20 -t 100 -k"
 
+ Boolean? skip_mark_dupes=false
+ Boolean? plot_only_non_duplicates=false
+
  command {
  set -ex -o pipefail
 
@@ -37,6 +40,7 @@ task plot_coverage {
  --GATK_PATH gatk/ \
  --aligner ${aligner} \
  --aligner_options "${aligner_options}" \
+ ${true='--skipMarkDupes' false="" skip_mark_dupes} \
  --JVMmemory=3g \
  --loglevel=DEBUG
 
@@ -56,6 +60,11 @@ task plot_coverage {
  # fastqc mapped bam
  reports.py fastqc ${sample_name}.mapped.bam ${sample_name}.mapped_fastqc.html
 
+ PLOT_DUPE_OPTION=""
+ if [[ "${skip_mark_dupes}" != "true" ]]; then
+ PLOT_DUPE_OPTION="${true='--plotOnlyNonDuplicates' false="" plot_only_non_duplicates}"
+ fi
+
  # plot coverage
  if [ $(cat reads_aligned) != 0 ]; then
  reports.py plot_coverage \
@@ -65,6 +74,7 @@ task plot_coverage {
  --plotWidth 1100 \
  --plotHeight 850 \
  --plotDPI 100 \
+ $PLOT_DUPE_OPTION \
  --plotTitle "${sample_name} coverage plot" \
  --loglevel=DEBUG
  else