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42 lines
1.8 KiB
Text
42 lines
1.8 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK_UNIFIEDGENOTYPER } from '../../../modules/gatk/unifiedgenotyper/main.nf'
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include { GUNZIP } from '../../../modules/gunzip/main.nf'
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include { MULTIVCFANALYZER } from '../../../modules/multivcfanalyzer/main.nf'
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workflow test_multivcfanalyzer {
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input = Channel.of([ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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],
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[ [ id:'test2' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
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],
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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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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
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mva_vcf = GUNZIP ( GATK_UNIFIEDGENOTYPER.out.vcf ).gunzip
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.map{it[1]}
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.collect()
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.dump()
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snpeff_results = []
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gff = []
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allele_freqs = true
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genotype_quality = 30
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coverage = 5
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homozygous_freq = 0.8
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heterozygous_freq = 0.2
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gff_exclude = []
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MULTIVCFANALYZER ( mva_vcf, fasta, snpeff_results, gff, allele_freqs, genotype_quality, coverage, homozygous_freq, heterozygous_freq, gff_exclude )
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}
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