kkonganti@0: // Include any necessary methods and modules
kkonganti@0: include { PRODIGAL                } from "${params.modules}${params.fs}prodigal${params.fs}main"
kkonganti@0: include { PROKKA                  } from "${params.modules}${params.fs}prokka${params.fs}main"
kkonganti@0: 
kkonganti@0: // Start the subworkflow
kkonganti@0: workflow PRODKA {
kkonganti@0:     take:
kkonganti@0:         trained_asm
kkonganti@0:         predict_asm
kkonganti@0: 
kkonganti@0:     main:
kkonganti@0:         PRODIGAL(
kkonganti@0:             trained_asm,
kkonganti@0:             (params.prodigal_f ?: 'gbk')
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         PROKKA( 
kkonganti@0:             predict_asm
kkonganti@0:                 .join(PRODIGAL.out.proteins)
kkonganti@0:                 .join(PRODIGAL.out.trained)
kkonganti@0:         )
kkonganti@0: 
kkonganti@0:         PRODIGAL.out.versions
kkonganti@0:             .mix( PROKKA.out.versions )
kkonganti@0:             .set{ versions }
kkonganti@0:     emit:
kkonganti@0:         prodigal_gene_annots     = PRODIGAL.out.gene_annotations
kkonganti@0:         prodigal_fna             = PRODIGAL.out.cds
kkonganti@0:         prodigal_faa             = PRODIGAL.out.proteins
kkonganti@0:         prodigal_all_gene_annots = PRODIGAL.out.all_gene_annotations
kkonganti@0:         prodigal_trained         = PRODIGAL.out.trained
kkonganti@0:         prokka_gff               = PROKKA.out.gff
kkonganti@0:         prokka_gbk               = PROKKA.out.gbk
kkonganti@0:         prokka_fna               = PROKKA.out.fna
kkonganti@0:         prokka_sqn               = PROKKA.out.sqn
kkonganti@0:         prokka_ffn               = PROKKA.out.ffn
kkonganti@0:         prokka_fsa               = PROKKA.out.fsa
kkonganti@0:         prokka_faa               = PROKKA.out.faa
kkonganti@0:         prokka_tbl               = PROKKA.out.tbl
kkonganti@0:         prokka_err               = PROKKA.out.err
kkonganti@0:         prokka_log               = PROKKA.out.log
kkonganti@0:         prokka_txt               = PROKKA.out.txt
kkonganti@0:         prokka_tsv               = PROKKA.out.tsv
kkonganti@0:         versions
kkonganti@0: }