1 files changed, 3 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
index f8da5d3..9d9b31d 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -16,6 +16,9 @@ stdout: $(inputs.readsFA.nameroot).sorted_by_quality_and_len.fasta
 outputs:
   sortedReadsFA:
     type: stdout
+  dups:
+    type: File
+    outputBinding: {glob: dups.txt}
 requirements:
   InlineJavascriptRequirement: {}
   ShellCommandRequirement: {}