Mercurial > repos > galaxytrakr > hfp_nowayout_awsbatch

comparison 0.5.0/subworkflows/prodka.nf @ 0:3c767f9cfd88 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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-1:000000000000 0:3c767f9cfd88
1 // Include any necessary methods and modules
2 include { PRODIGAL } from "${params.modules}${params.fs}prodigal${params.fs}main"
3 include { PROKKA } from "${params.modules}${params.fs}prokka${params.fs}main"
4
5 // Start the subworkflow
6 workflow PRODKA {
7 take:
8 trained_asm
9 predict_asm
10
11 main:
12 PRODIGAL(
13 trained_asm,
14 (params.prodigal_f ?: 'gbk')
15 )
16
17 PROKKA(
18 predict_asm
19 .join(PRODIGAL.out.proteins)
20 .join(PRODIGAL.out.trained)
21 )
22
23 PRODIGAL.out.versions
24 .mix( PROKKA.out.versions )
25 .set{ versions }
26 emit:
27 prodigal_gene_annots = PRODIGAL.out.gene_annotations
28 prodigal_fna = PRODIGAL.out.cds
29 prodigal_faa = PRODIGAL.out.proteins
30 prodigal_all_gene_annots = PRODIGAL.out.all_gene_annotations
31 prodigal_trained = PRODIGAL.out.trained
32 prokka_gff = PROKKA.out.gff
33 prokka_gbk = PROKKA.out.gbk
34 prokka_fna = PROKKA.out.fna
35 prokka_sqn = PROKKA.out.sqn
36 prokka_ffn = PROKKA.out.ffn
37 prokka_fsa = PROKKA.out.fsa
38 prokka_faa = PROKKA.out.faa
39 prokka_tbl = PROKKA.out.tbl
40 prokka_err = PROKKA.out.err
41 prokka_log = PROKKA.out.log
42 prokka_txt = PROKKA.out.txt
43 prokka_tsv = PROKKA.out.tsv
44 versions
45 }