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acb1a12a56
* Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
18 lines
817 B
Text
18 lines
817 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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input = [ [ id:'test' ], // meta map
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[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/vcf/test.vcf", 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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GATK4_VARIANTFILTRATION ( input, fasta )
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}
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