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* Add centrifuge module * Add centrifuge module * Add centrifuge module * Add centrifuge module
33 lines
1.2 KiB
Text
33 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'
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workflow test_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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CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
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}
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workflow test_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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CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
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}
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