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