Mercurial > repos > kkonganti > hfp_nowayout
annotate 0.5.0/subworkflows/prodka.nf @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 // Include any necessary methods and modules |
| kkonganti@0 | 2 include { PRODIGAL } from "${params.modules}${params.fs}prodigal${params.fs}main" |
| kkonganti@0 | 3 include { PROKKA } from "${params.modules}${params.fs}prokka${params.fs}main" |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 // Start the subworkflow |
| kkonganti@0 | 6 workflow PRODKA { |
| kkonganti@0 | 7 take: |
| kkonganti@0 | 8 trained_asm |
| kkonganti@0 | 9 predict_asm |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 main: |
| kkonganti@0 | 12 PRODIGAL( |
| kkonganti@0 | 13 trained_asm, |
| kkonganti@0 | 14 (params.prodigal_f ?: 'gbk') |
| kkonganti@0 | 15 ) |
| kkonganti@0 | 16 |
| kkonganti@0 | 17 PROKKA( |
| kkonganti@0 | 18 predict_asm |
| kkonganti@0 | 19 .join(PRODIGAL.out.proteins) |
| kkonganti@0 | 20 .join(PRODIGAL.out.trained) |
| kkonganti@0 | 21 ) |
| kkonganti@0 | 22 |
| kkonganti@0 | 23 PRODIGAL.out.versions |
| kkonganti@0 | 24 .mix( PROKKA.out.versions ) |
| kkonganti@0 | 25 .set{ versions } |
| kkonganti@0 | 26 emit: |
| kkonganti@0 | 27 prodigal_gene_annots = PRODIGAL.out.gene_annotations |
| kkonganti@0 | 28 prodigal_fna = PRODIGAL.out.cds |
| kkonganti@0 | 29 prodigal_faa = PRODIGAL.out.proteins |
| kkonganti@0 | 30 prodigal_all_gene_annots = PRODIGAL.out.all_gene_annotations |
| kkonganti@0 | 31 prodigal_trained = PRODIGAL.out.trained |
| kkonganti@0 | 32 prokka_gff = PROKKA.out.gff |
| kkonganti@0 | 33 prokka_gbk = PROKKA.out.gbk |
| kkonganti@0 | 34 prokka_fna = PROKKA.out.fna |
| kkonganti@0 | 35 prokka_sqn = PROKKA.out.sqn |
| kkonganti@0 | 36 prokka_ffn = PROKKA.out.ffn |
| kkonganti@0 | 37 prokka_fsa = PROKKA.out.fsa |
| kkonganti@0 | 38 prokka_faa = PROKKA.out.faa |
| kkonganti@0 | 39 prokka_tbl = PROKKA.out.tbl |
| kkonganti@0 | 40 prokka_err = PROKKA.out.err |
| kkonganti@0 | 41 prokka_log = PROKKA.out.log |
| kkonganti@0 | 42 prokka_txt = PROKKA.out.txt |
| kkonganti@0 | 43 prokka_tsv = PROKKA.out.tsv |
| kkonganti@0 | 44 versions |
| kkonganti@0 | 45 } |