update flu output

workflows/utilities/wf_flu_track.wdl

@@ -112,16 +112,12 @@ workflow flu_track {
         docker = assembly_metrics_docker
     }
   }
-  # Calculate the percentage of mapped reads for flu samples
-  if (defined(irma.seg_ha_bam) || defined(irma.seg_na_bam)) {
-    call assembly_metrics.stats_n_coverage as flu_stats_n_coverage {
-      input:
-        samplename = samplename,
-        bamfile = select_first([irma.seg_ha_bam, irma.seg_na_bam])
-    }
-  }
   # combine HA & NA assembly coverages
   String ha_na_assembly_coverage_string = "HA: " + select_first([ha_assembly_coverage.depth, ""]) + ", NA: " + select_first([na_assembly_coverage.depth, ""])
+
+  # combine HA & NA mapped reads percentages
+  String ha_na_mapped_reads_percentage_string = "HA: " + select_first([ha_assembly_coverage.percentage_mapped_reads, ""]) + ", NA: " + select_first([na_assembly_coverage.percentage_mapped_reads, ""])
+
   # ABRICATE will run if assembly is provided, or was generated with IRMA
   if (defined(irma.irma_assemblies) && defined(irma.irma_assembly_fasta)){
     call abricate.abricate_flu {
@@ -264,7 +260,7 @@ workflow flu_track {
     File? irma_na_bam = irma.seg_na_bam
     String ha_na_assembly_coverage = ha_na_assembly_coverage_string
      # calulate mapped reads percentage for flu samples
-    Float? percentage_mapped_reads = flu_stats_n_coverage.percentage_mapped_reads
+    String percentage_mapped_reads = flu_stats_n_coverage.percentage_mapped_reads
     # GenoFLU outputs
     String? genoflu_version = genoflu.genoflu_version
     String? genoflu_genotype = genoflu.genoflu_genotype