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Output concatenated ffn files from Prokka #186

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merged 2 commits into from
Sep 26, 2023
Merged

Output concatenated ffn files from Prokka #186

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cb095ac
Output concatenated ffn files from Prokka
erikrikarddaniel Sep 26, 2023
be351ba
Remove concatenation of Prokka fna files
erikrikarddaniel Sep 26, 2023
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4 changes: 2 additions & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -192,8 +192,8 @@ process {
]
}

withName: 'FNA_CAT' {
ext.prefix = 'prokka.fna.gz'
withName: 'FFN_CAT' {
ext.prefix = 'prokka.ffn.gz'
publishDir = [
path: { "${params.outdir}/prokka" },
mode: 'copy',
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12 changes: 6 additions & 6 deletions subworkflows/local/prokka_subsets.nf
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Expand Up @@ -5,7 +5,7 @@
include { PROKKA } from '../../modules/nf-core/prokka/main'
include { CAT_CAT as GFF_CAT } from '../../modules/nf-core/cat/cat/main'
include { CAT_CAT as FAA_CAT } from '../../modules/nf-core/cat/cat/main'
include { CAT_CAT as FNA_CAT } from '../../modules/nf-core/cat/cat/main'
include { CAT_CAT as FFN_CAT } from '../../modules/nf-core/cat/cat/main'
include { PROKKAGFF2TSV } from '../../modules/local/prokkagff2tsv'

workflow PROKKA_SUBSETS {
Expand All @@ -32,18 +32,18 @@ workflow PROKKA_SUBSETS {
ch_versions = ch_versions.mix(FAA_CAT.out.versions)

contigs.map{ [ id:"${it[0].id}.prokka" ] }
.combine(PROKKA.out.fna.collect { it[1] }.map { [ it ] })
.set { ch_fna }
FNA_CAT ( ch_fna )
ch_versions = ch_versions.mix(FNA_CAT.out.versions)
.combine(PROKKA.out.ffn.collect { it[1] }.map { [ it ] })
.set { ch_ffn }
FFN_CAT ( ch_ffn )
ch_versions = ch_versions.mix(FFN_CAT.out.versions)

PROKKAGFF2TSV ( GFF_CAT.out.file_out)
ch_versions = ch_versions.mix(PROKKAGFF2TSV.out.versions)

emit:
gff = GFF_CAT.out.file_out
faa = FAA_CAT.out.file_out
fna = FNA_CAT.out.file_out
ffn = FFN_CAT.out.file_out
gfftsv = PROKKAGFF2TSV.out.tsv
prokka_log = ch_log
versions = ch_versions
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