--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/subworkflows/prodka.nf	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,45 @@
+// Include any necessary methods and modules
+include { PRODIGAL                } from "${params.modules}${params.fs}prodigal${params.fs}main"
+include { PROKKA                  } from "${params.modules}${params.fs}prokka${params.fs}main"
+
+// Start the subworkflow
+workflow PRODKA {
+    take:
+        trained_asm
+        predict_asm
+
+    main:
+        PRODIGAL(
+            trained_asm,
+            (params.prodigal_f ?: 'gbk')
+        )
+
+        PROKKA( 
+            predict_asm
+                .join(PRODIGAL.out.proteins)
+                .join(PRODIGAL.out.trained)
+        )
+
+        PRODIGAL.out.versions
+            .mix( PROKKA.out.versions )
+            .set{ versions }
+    emit:
+        prodigal_gene_annots     = PRODIGAL.out.gene_annotations
+        prodigal_fna             = PRODIGAL.out.cds
+        prodigal_faa             = PRODIGAL.out.proteins
+        prodigal_all_gene_annots = PRODIGAL.out.all_gene_annotations
+        prodigal_trained         = PRODIGAL.out.trained
+        prokka_gff               = PROKKA.out.gff
+        prokka_gbk               = PROKKA.out.gbk
+        prokka_fna               = PROKKA.out.fna
+        prokka_sqn               = PROKKA.out.sqn
+        prokka_ffn               = PROKKA.out.ffn
+        prokka_fsa               = PROKKA.out.fsa
+        prokka_faa               = PROKKA.out.faa
+        prokka_tbl               = PROKKA.out.tbl
+        prokka_err               = PROKKA.out.err
+        prokka_log               = PROKKA.out.log
+        prokka_txt               = PROKKA.out.txt
+        prokka_tsv               = PROKKA.out.tsv
+        versions
+}