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https://github.com/MillironX/nf-core_modules.git
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a552d97849
* added sarscov2 vcf data; adjusted bcftools tests * updated README.md * deleted old VCF files; fixed mergevcfs * fixed tabix
27 lines
1 KiB
Text
27 lines
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("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
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ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.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("${launchDir}/tests/data/genomics/sarscov2/vcf/test.vcf", checkIfExists: true),
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file("${launchDir}/tests/data/genomics/sarscov2/vcf/test2.vcf", checkIfExists: true) ] ]
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ref_dict = file('tests/data/genomics/sarscov2/fasta/test_genome.dict', checkIfExists: true)
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GATK4_MERGEVCFS ( input, ref_dict, true )
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}
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