fix(HRD, TMB): output

tasks/HRD.wdl

@@ -46,25 +46,25 @@ task HRD {
   }
   
   output {
-    hrd="${sample}.HRD.txt"
-    alternative_fit="${sample}_alternative_fit.pdf"
-    alternative_solutions="${sample}_alternative_solutions.txt"
-    chromosome_depths="${sample}_chromosome_depths.pdf"
-    chromosome_view="${sample}_chromosome_view.pdf"
-    CN_bars="${sample}_CN_bars.pdf"
-    confints_CP="${sample}_confints_CP.txt"
-    contours_CP="${sample}_contours_CP.pdf"
-    CP_contours="${sample}_CP_contours.pdf"
-    gc_plots="${sample}_gc_plots.pdf"
-    genome_view="${sample}_genome_view.pdf"
-    model_fit="${sample}_model_fit.pdf"
-    mutations="${sample}_mutations.txt"
-    scarHRD_input="${sample}_scarHRD_input.txt"
-    segments="${sample}_segments.txt"
-    sequenza_cp_table="${sample}_sequenza_cp_table.RData"
-    sequenza_extract="${sample}_sequenza_extract.RData"
-    sequenza_log="${sample}_sequenza_log.txt"
-    small_seqz="${sample}.small.seqz.gz"
-    small_seqz_index="${sample}.small.seqz.gz.tbi"
+    File hrd="${sample}.HRD.txt"
+    File alternative_fit="${sample}_alternative_fit.pdf"
+    File alternative_solutions="${sample}_alternative_solutions.txt"
+    File chromosome_depths="${sample}_chromosome_depths.pdf"
+    File chromosome_view="${sample}_chromosome_view.pdf"
+    File CN_bars="${sample}_CN_bars.pdf"
+    File confints_CP="${sample}_confints_CP.txt"
+    File contours_CP="${sample}_contours_CP.pdf"
+    File CP_contours="${sample}_CP_contours.pdf"
+    File gc_plots="${sample}_gc_plots.pdf"
+    File genome_view="${sample}_genome_view.pdf"
+    File model_fit="${sample}_model_fit.pdf"
+    File mutations="${sample}_mutations.txt"
+    File scarHRD_input="${sample}_scarHRD_input.txt"
+    File segments="${sample}_segments.txt"
+    File sequenza_cp_table="${sample}_sequenza_cp_table.RData"
+    File sequenza_extract="${sample}_sequenza_extract.RData"
+    File sequenza_log="${sample}_sequenza_log.txt"
+    File small_seqz="${sample}.small.seqz.gz"
+    File small_seqz_index="${sample}.small.seqz.gz.tbi"
   }
 }

tasks/TMB.wdl

@@ -26,7 +26,7 @@ task TMB {
   }
   
   output {
-    snp_indel="${sample}.snp_indel.txt"
-    tmb="${sample}.TMB.txt"
+    File snp_indel="${sample}.snp_indel.txt"
+    File tmb="${sample}.TMB.txt"
   }
 }