Save the GFA file too

broadinstitute · Oct 15, 2024 · c2404d6 · c2404d6
1 parent 82e6d60
commit c2404d6
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/wdl/HidiveCorrect.wdl b/wdl/HidiveCorrect.wdl
@@ -143,11 +143,12 @@ task Correct {
     command <<<
         set -euxo pipefail
 
-        hidive correct -m ~{model} ~{short_read_fasta} ~{long_read_fasta} > ~{prefix}.fa
+        hidive correct -m ~{model} -g {prefix}.gfa ~{long_read_fasta} ~{short_read_fasta} > ~{prefix}.fa
     >>>
 
     output {
         File fasta = "~{prefix}.fa"
+        File gfa = "~{prefix}.gfa"
     }
 
     runtime {