step 06

subworkflows/shared.nf

@@ -17,15 +17,15 @@ workflow SHARED {
     ch_prokka_reads = Channel.empty()
     ch_prokka_faa = Channel.empty()
     if ( ! params.skip_structural_annot ) {
-        PROKKA_AND_RENAME (ch_assembly)
-        ch_prokka_reads = PROKKA_AND_RENAME.out.gff.join(PROKKA_AND_RENAME.out.fna, remainder: true).join(ch_reads, remainder: true)
-        ch_prokka_faa = PROKKA_AND_RENAME.out.faa
+        STEP_04_STRUCTURAL_ANNOT (ch_assembly)
+        ch_prokka_reads = STEP_04_STRUCTURAL_ANNOT.out.gff.join(STEP_04_STRUCTURAL_ANNOT.out.fna, remainder: true).join(ch_reads, remainder: true)
+        ch_prokka_faa = STEP_04_STRUCTURAL_ANNOT.out.faa
     }
     if ( ! params.skip_alignment) {
         STEP_05_ALIGNMENT(ch_prokka_reads, ch_prokka_faa)
     }
     if ( ! params.skip_func_annot) {
-        STEP_06_FUNC_ANNOT(PROKKA_AND_RENAME.out.fna)
+        STEP_06_FUNC_ANNOT(STEP_04_STRUCTURAL_ANNOT.out.fna)
     }
     
 	emit: