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32 lines
1.6 KiB
Text
32 lines
1.6 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf' addParams( options: [:] )
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workflow test_gatk4_getpileupsummaries_just_variants {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
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variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
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variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
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sites = []
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GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
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}
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workflow test_gatk4_getpileupsummaries_separate_sites {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ]
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variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
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variants_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
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sites = file( "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.interval_list" , checkIfExists: true)
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GATK4_GETPILEUPSUMMARIES ( input , variants , variants_idx , sites )
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}
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