fix cupGenerateReport

hmftools.wdl

@@ -195,15 +195,19 @@ task CupGenerateReport {
         ~{sampleName} \
         workdir/
         mv -t ~{outputDir} \
-        ./workdir/~{sampleName}.cup.report.summry.png \
-        ./workdir/~{sampleName}.cup.report.features.png \
-        ./workdir/~{sampleName}_cup.report.pdf
+        ./workdir/~{sampleName}.cup.report.summary.png \
+        ./workdir/~{sampleName}_cup_report.pdf
+        if [ -f ./workdir/~{sampleName}.cup.report.features.png ]
+          then
+            mv -t ~{outputDir} \
+            ./workdir/~{sampleName}.cup.report.features.png
+        fi
     }
 
     output {
-        File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summry.png"
-        File featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
-        File reportPdf = "~{outputDir}/~{sampleName}_cup.report.pdf"
+        File summaryPng = "~{outputDir}/~{sampleName}.cup.report.summary.png"
+        File? featuresPng = "~{outputDir}/~{sampleName}.cup.report.features.png"
+        File reportPdf = "~{outputDir}/~{sampleName}_cup_report.pdf"
     }
 
     runtime {
@@ -765,7 +769,7 @@ task Orange {
         Array[File]+ linxPlots
         File cuppaResultCsv
         File cuppaSummaryPlot
-        File cuppaFeaturePlot
+        File? cuppaFeaturePlot
         File chordPredictionTxt
         File peachGenotypeTsv
         File protectEvidenceTsv
@@ -812,7 +816,7 @@ task Orange {
         -linx_plot_directory ~{sub(linxPlots[0], basename(linxPlots[0]), "")} \
         -cuppa_result_csv ~{cuppaResultCsv} \
         -cuppa_summary_plot ~{cuppaSummaryPlot} \
-        -cuppa_feature_plot ~{cuppaFeaturePlot} \
+        ~{"-cuppa_feature_plot " + cuppaFeaturePlot} \
         -chord_prediction_txt ~{chordPredictionTxt} \
         -peach_genotype_tsv ~{peachGenotypeTsv} \
         -protect_evidence_tsv ~{protectEvidenceTsv} \
@@ -861,7 +865,7 @@ task Orange {
         linxPlots: {description: "The plots generated by linx.", category: "required"}
         cuppaResultCsv: {description: "The cuppa results csv.", category: "required"}
         cuppaSummaryPlot: {description: "The cuppa summary plot.", category: "required"}
-        cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "required"}
+        cuppaFeaturePlot: {description: "The cuppa feature plot.", category: "common"}
         chordPredictionTxt: {description: "Chord prediction results.", category: "required"}
         peachGenotypeTsv: {description: "Genotype tsv produced by peach.", category: "required"}
         protectEvidenceTsv: {description: "Evidence tsv produced by protect.", category: "required"}