2021-02-19 13:59:29 +00:00
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_SPLITNCIGARREADS } from '../../../../software/gatk4/splitncigarreads/main.nf' addParams( options: [:] )
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workflow test_gatk4_splitncigarreads {
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input = [ [ id:'test' ], // 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/bam/test_paired_end.bam", checkIfExists: true)]
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]
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fasta = [ file("tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true),
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file("tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true),
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file("tests/data/genomics/sarscov2/genome/genome.dict", checkIfExists: true)
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]
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2021-02-19 13:59:29 +00:00
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2021-02-22 12:31:54 +00:00
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GATK4_SPLITNCIGARREADS ( input, fasta )
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2021-02-19 13:59:29 +00:00
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}
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