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36 lines
1.4 KiB
Text
36 lines
1.4 KiB
Text
#!/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 { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf'
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workflow test_centrifuge_centrifuge_single_end {
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input = [ [ 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('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
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save_unaligned = true
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save_aligned = false
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sam_format = false
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UNTAR ( db )
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CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
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}
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workflow test_centrifuge_centrifuge_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
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save_unaligned = true
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save_aligned = false
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sam_format = false
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UNTAR ( db )
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CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
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}
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