Merge pull request #218 from biowdl/BIOWDL-465

BIOWDL-465: Make a number of outputs optional in Picard.

CHANGELOG.md

@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
 
 version 3.2.0-develop
 ---------------------------
++ Picard: Make all outputs in `CollectMultipleMetrics` optional. This will make sure the
+  task will not fail if one of the metrics is set to false.
 + The struct `BowtieIndex` was removed, as it has become obsolete.
 + The task `ReorderGlobbedScatters` was removed, as it has become obsolete.
 + Adjusted the memory settings of many tools, especially java tools.

picard.wdl

@@ -113,24 +113,24 @@ task CollectMultipleMetrics {
     }
 
     output {
-        File alignmentSummary = basename + ".alignment_summary_metrics"
-        File baitBiasDetail = basename + ".bait_bias_detail_metrics"
-        File baitBiasSummary = basename + ".bait_bias_summary_metrics"
-        File baseDistributionByCycle = basename + ".base_distribution_by_cycle_metrics"
-        File baseDistributionByCyclePdf = basename + ".base_distribution_by_cycle.pdf"
-        File errorSummary = basename + ".error_summary_metrics"
-        File gcBiasDetail = basename + ".gc_bias.detail_metrics"
-        File gcBiasPdf = basename + ".gc_bias.pdf"
-        File gcBiasSummary = basename + ".gc_bias.summary_metrics"
+        File? alignmentSummary = basename + ".alignment_summary_metrics"
+        File? baitBiasDetail = basename + ".bait_bias_detail_metrics"
+        File? baitBiasSummary = basename + ".bait_bias_summary_metrics"
+        File? baseDistributionByCycle = basename + ".base_distribution_by_cycle_metrics"
+        File? baseDistributionByCyclePdf = basename + ".base_distribution_by_cycle.pdf"
+        File? errorSummary = basename + ".error_summary_metrics"
+        File? gcBiasDetail = basename + ".gc_bias.detail_metrics"
+        File? gcBiasPdf = basename + ".gc_bias.pdf"
+        File? gcBiasSummary = basename + ".gc_bias.summary_metrics"
         File? insertSizeHistogramPdf = basename + ".insert_size_histogram.pdf"
         File? insertSize = basename + ".insert_size_metrics"
-        File preAdapterDetail = basename + ".pre_adapter_detail_metrics"
-        File preAdapterSummary = basename + ".pre_adapter_summary_metrics"
-        File qualityByCycle = basename + ".quality_by_cycle_metrics"
-        File qualityByCyclePdf = basename + ".quality_by_cycle.pdf"
-        File qualityDistribution = basename + ".quality_distribution_metrics"
-        File qualityDistributionPdf = basename + ".quality_distribution.pdf"
-        File qualityYield = basename + ".quality_yield_metrics"
+        File? preAdapterDetail = basename + ".pre_adapter_detail_metrics"
+        File? preAdapterSummary = basename + ".pre_adapter_summary_metrics"
+        File? qualityByCycle = basename + ".quality_by_cycle_metrics"
+        File? qualityByCyclePdf = basename + ".quality_by_cycle.pdf"
+        File? qualityDistribution = basename + ".quality_distribution_metrics"
+        File? qualityDistributionPdf = basename + ".quality_distribution.pdf"
+        File? qualityYield = basename + ".quality_yield_metrics"
         # Using a glob is easier. But will lead to very ugly output directories.
         Array[File] allStats = select_all([
             alignmentSummary,