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31 lines
1.1 KiB
Text
31 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_MERGEVCFS } from '../../../../software/gatk4/mergevcfs/main.nf' addParams( options: [:] )
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workflow test_gatk4_mergevcfs {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
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file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
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file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
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ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
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GATK4_MERGEVCFS ( input, ref_dict, false )
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}
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workflow test_gatk4_mergevcfs_refdict {
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def input = []
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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true),
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file("${launchDir}/tests/data/vcf/test2.vcf.gz", checkIfExists: true),
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file("${launchDir}/tests/data/vcf/test3.vcf.gz", checkIfExists: true) ] ]
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ref_dict = file("tests/data/fasta/test.consensus.for_vcf.dict", checkIfExists: true)
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GATK4_MERGEVCFS ( input, ref_dict, true )
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}
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