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45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
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workflow test_spades_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_2_fastq_gz'], checkIfExists: true) ]
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]
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coronaspades = false
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SPADES ( input, [], coronaspades )
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}
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workflow test_spades_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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coronaspades = false
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SPADES ( input, [], coronaspades )
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}
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workflow test_coronospades_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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coronaspades = true
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SPADES ( input, [], coronaspades )
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}
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workflow test_coronospades_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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coronaspades = true
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SPADES ( input, [], coronaspades )
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}
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