2021-03-22 18:26:02 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_FASTQTOSAM } from '../../../../software/gatk4/fastqtosam/main.nf' addParams( options: [:] )
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workflow test_gatk4_fastqtosam_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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2021-03-24 09:53:41 +00:00
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
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]
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2021-03-22 18:26:02 +00:00
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GATK4_FASTQTOSAM ( input )
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}
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workflow test_gatk4_fastqtosam_paired_end {
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input = [ [ id:'test', single_end:false ], // meta map
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2021-03-24 09:53:41 +00:00
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)
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]
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2021-03-22 18:26:02 +00:00
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GATK4_FASTQTOSAM ( input )
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}
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