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22 lines
786 B
Text
22 lines
786 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../modules/untar/main.nf'
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include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
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include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
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workflow test_kaiju_kaiju_single_end {
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input = [
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[ id:'test', single_end:true ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
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taxon_rank = "species"
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ch_db = UNTAR ( db )
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KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
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KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
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}
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