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https://github.com/MillironX/nf-core_modules.git
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43a1c1c6d1
* Added vcf_index to vcf tuple; output to vcf.gz format. * Fix: extra new line in meta.yml. * addressed review feedback * fix: editorconfig error * fix: gatk memory flag * fix: editorconfig error * fix: Indentation fix: Indentation * Fix: lint editorconfig error Removed one extra space Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
36 lines
1.7 KiB
Text
36 lines
1.7 KiB
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 '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
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// Basic parameters with uncompressed VCF input
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workflow test_gatk4_variantfiltration_vcf_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true) ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
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}
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// Basic parameters with compressed VCF input
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workflow test_gatk4_variantfiltration_gz_input {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) ]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fastaIndex = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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fastaDict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_VARIANTFILTRATION ( input, fasta, fastaIndex, fastaDict )
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}
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