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21 lines
722 B
Text
21 lines
722 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_KAIJU2KRONA } from '../../../../modules/kaiju/kaiju2krona/main.nf'
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workflow test_kaiju_kaiju2krona {
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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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UNTAR ( db )
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KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
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KAIJU_KAIJU2KRONA ( KAIJU_KAIJU.out.results , UNTAR.out.untar.map{ it[1] } )
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}
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