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remove whitespaces on line 74
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subworkflows/local/prepare_genome.nf

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -71,18 +71,21 @@ workflow PREPARE_GENOME {
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}
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}
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else if (gff) {
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if (gff.endsWith('.gz')) {
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if (gff.endsWith('.gz')) {
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ch_gff = GUNZIP_GFF([[:], file(gff, checkIfExists: true)]).gunzip.map { it[1] }
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ch_versions = ch_versions.mix(GUNZIP_GFF.out.versions)
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}
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else {
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ch_gff = Channel.value(file(gff, checkIfExists: true))
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}
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//
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// Detect gff file name stripped of extension and .gz
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//
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extension = (gff - '.gz').tokenize('.')[-1]
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id = gff.toString() - '.gz' - ".${extension}"
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ch_gtf = GFFREAD(ch_gff.map{[[id:id], it]}, []).gtf.map { it[1] }
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ch_gtf = GFFREAD(ch_gff.map { [[id: id], it] }, []).gtf.map { it[1] }
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ch_versions = ch_versions.mix(GFFREAD.out.versions)
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}

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