correctly name percentage mapped reads

theiagen · Nov 4, 2024 · 1b58829 · 1b58829
1 parent 8b8aea1
commit 1b58829
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/workflows/theiacov/wf_theiacov_ont.wdl b/workflows/theiacov/wf_theiacov_ont.wdl
@@ -428,6 +428,6 @@ workflow theiacov_ont {
     String? qc_check = qc_check_task.qc_check
     File? qc_standard = qc_check_task.qc_standard
     # Non-flu specific outputs
-    String percentage_mapped_reads = select_first([stats_n_coverage.percentage_mapped_reads, flu_track.ha_na_mapped_reads_percentage, ""])
+    String percentage_mapped_reads = select_first([stats_n_coverage.percentage_mapped_reads, flu_track.ha_na_percentage_mapped_reads, ""])
   }
 }
diff --git a/workflows/utilities/wf_flu_track.wdl b/workflows/utilities/wf_flu_track.wdl
@@ -116,7 +116,7 @@ workflow flu_track {
   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, ""])
+  String ha_na_percentage_mapped_reads = "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)){