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889465cb2b
* update test data paths * Update test md5sums * gatk test fixes & update variantfiltration main * few extra fixes after review * fix suspected format error * Update software/gatk4/variantfiltration/main.nf * Update software/gatk4/variantfiltration/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
18 lines
851 B
Text
18 lines
851 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"', 'suffix': '.filtered']
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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(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
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]
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fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
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genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
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GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
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}
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