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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { LEEHOM } from '../../../modules/leehom/main.nf' addParams( options: [:] )
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include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' addParams( options: [args: "-f4 -b"] )
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workflow test_leehom_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ]
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fasta = []
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SAMTOOLS_VIEW ( input, fasta )
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LEEHOM ( SAMTOOLS_VIEW.out.bam )
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}
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workflow test_leehom_se_fq {
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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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LEEHOM ( input )
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}
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workflow test_leehom_pe_fq {
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input = [ [ id:'test', single_end:false ], // meta map
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[
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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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LEEHOM ( input )
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}
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