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26 lines
1.3 KiB
Text
26 lines
1.3 KiB
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 { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
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include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
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include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../../../modules/bracken/combinebrackenoutputs/main.nf'
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workflow test_bracken_combinebrackenoutputs {
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input = Channel.of(
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[[ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
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[[ id:'test2', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]],
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)
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db = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
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ch_db = UNTAR ( [[:], db] ).untar
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.map { it[1] }
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KRAKEN2_KRAKEN2 ( input, ch_db, false, false )
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BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.report, ch_db )
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BRACKEN_COMBINEBRACKENOUTPUTS ( BRACKEN_BRACKEN.out.reports.map{it[1]}.collect() )
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}
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