fix purple outputs

hmftools.wdl

@@ -838,11 +838,13 @@ task Purple {
     }
 
     output {
-        File driverCatalogSomaticTsv = "~{outputDir}/~{tumorName}.driver.catalog.somatic.tsv"
         File driverCatalogGermlineTsv = "~{outputDir}/~{tumorName}.driver.catalog.germline.tsv"
+        File driverCatalogSomaticTsv = "~{outputDir}/~{tumorName}.driver.catalog.somatic.tsv"
         File purpleCnvGeneTsv = "~{outputDir}/~{tumorName}.purple.cnv.gene.tsv"
-        File purpleCnvGermlineTsv = "~{outputDir}/~{tumorName}.purple.cnv.germline.tsv"
         File purpleCnvSomaticTsv = "~{outputDir}/~{tumorName}.purple.cnv.somatic.tsv"
+        File purpleGermlineDeletionTsv = "~{outputDir}/~{tumorName}.purple.germline.deletion.tsv"
+        File purpleGermlineVcf = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz"
+        File purpleGermlineVcfIndex = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz.tbi"
         File purplePurityRangeTsv = "~{outputDir}/~{tumorName}.purple.purity.range.tsv"
         File purplePurityTsv = "~{outputDir}/~{tumorName}.purple.purity.tsv"
         File purpleQc = "~{outputDir}/~{tumorName}.purple.qc"
@@ -851,10 +853,9 @@ task Purple {
         File purpleSomaticHistTsv = "~{outputDir}/~{tumorName}.purple.somatic.hist.tsv"
         File purpleSomaticVcf = "~{outputDir}/~{tumorName}.purple.somatic.vcf.gz"
         File purpleSomaticVcfIndex = "~{outputDir}/~{tumorName}.purple.somatic.vcf.gz.tbi"
-        File purpleGermlineVcf = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz"
-        File purpleGermlineVcfIndex = "~{outputDir}/~{tumorName}.purple.germline.vcf.gz.tbi"
         File purpleSvVcf = "~{outputDir}/~{tumorName}.purple.sv.vcf.gz"
         File purpleSvVcfIndex = "~{outputDir}/~{tumorName}.purple.sv.vcf.gz.tbi"
+        File purpleVersion = "~{outputDir}/purple.version"
         File circosPlot = "~{outputDir}/plot/~{tumorName}.circos.png"
         File copynumberPlot = "~{outputDir}/plot/~{tumorName}.copynumber.png"
         File inputPlot = "~{outputDir}/plot/~{tumorName}.input.png"
@@ -863,19 +864,19 @@ task Purple {
         File segmentPlot = "~{outputDir}/plot/~{tumorName}.segment.png"
         File somaticClonalityPlot = "~{outputDir}/plot/~{tumorName}.somatic.clonality.png"
         File somaticPlot = "~{outputDir}/plot/~{tumorName}.somatic.png"
-        File purpleVersion = "~{outputDir}/purple.version"
+        File somaticRainfallPlot = "~{outputDir}/plot/~{tumorName}.somatic.rainfall.png"
         File circosNormalRatio = "~{outputDir}/circos/~{referenceName}.ratio.circos"
-        File circosConf = "~{outputDir}/circos/~{tumorName}.circos.conf"
-        File circosIndel = "~{outputDir}/circos/~{tumorName}.indel.circos"
-        File circosLink = "~{outputDir}/circos/~{tumorName}.link.circos"
-        File circosTumorRatio = "~{outputDir}/circos/~{tumorName}.ratio.circos"
-        File circosGaps = "~{outputDir}/circos/gaps.txt"
         File circosBaf = "~{outputDir}/circos/~{tumorName}.baf.circos"
+        File circosConf = "~{outputDir}/circos/~{tumorName}.circos.conf"
         File circosCnv = "~{outputDir}/circos/~{tumorName}.cnv.circos"
+        File circosIndel = "~{outputDir}/circos/~{tumorName}.indel.circos"
         File circosInputConf = "~{outputDir}/circos/~{tumorName}.input.conf"
+        File circosLink = "~{outputDir}/circos/~{tumorName}.link.circos"
         File circosMap = "~{outputDir}/circos/~{tumorName}.map.circos"
+        File circosTumorRatio = "~{outputDir}/circos/~{tumorName}.ratio.circos"
         File circosSnp = "~{outputDir}/circos/~{tumorName}.snp.circos"
-        Array[File] outputs = [driverCatalogSomaticTsv, purpleCnvGeneTsv, purpleCnvGermlineTsv,
+        File circosGaps = "~{outputDir}/circos/gaps.txt"
+        Array[File] outputs = [driverCatalogSomaticTsv, purpleCnvGeneTsv,
             purpleCnvSomaticTsv, purplePurityRangeTsv, purplePurityTsv, purpleQc,
             purpleSegmentTsv, purpleSomaticClonalityTsv, purpleSomaticHistTsv,
             purpleSomaticVcf, purpleSomaticVcfIndex, purpleSvVcf, purpleSvVcfIndex,