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group krakenuniq reads by pairs or single end
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@ -269,6 +269,16 @@ workflow PROFILING {
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if ( params.run_krakenuniq ) {
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ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
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.map {
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meta, reads, db_meta, db ->
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def meta_new = [:]
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meta_new['tool'] = meta['tool']
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meta_new['single_end'] = meta['single_end']
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[meta_new, reads, db_meta, db]
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}
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.groupTuple(by: [0,2,3])
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.dump(tag: "krakenuniq_premultimap")
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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