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17dbff52f4
* added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
18 lines
813 B
Text
18 lines
813 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"']
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include { GATK4_VARIANTFILTRATION } from '../../../../software/gatk4/variantfiltration/main.nf' addParams( options: test_options )
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workflow test_gatk4_variantfiltration {
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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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fasta = [ file("tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true),
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file("tests/data/genomics/sarscov2/fasta/test_genome.fasta.fai", checkIfExists: true),
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file("tests/data/genomics/sarscov2/fasta/test_genome.dict", checkIfExists: true)]
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GATK4_VARIANTFILTRATION ( input, fasta )
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}
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