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30 lines
1.2 KiB
Text
30 lines
1.2 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
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include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
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include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
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workflow test_snapaligner_single {
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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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SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
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SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
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}
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workflow test_snapaligner_paired {
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input = [
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[ id:'test', single_end:false ], // meta map
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[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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SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
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SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
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}
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