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57 lines
2 KiB
Text
57 lines
2 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_COLLECTSVEVIDENCE } from '../../../../modules/gatk4/collectsvevidence/main.nf'
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workflow test_gatk4_collectsvevidence_cram {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
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}
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workflow test_gatk4_collectsvevidence_bam {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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]
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fasta = []
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fasta_fai = []
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dict = []
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GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
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}
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workflow test_gatk4_collectsvevidence_allele_count {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true)
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]
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fasta = []
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fasta_fai = []
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dict = []
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GATK4_COLLECTSVEVIDENCE ( input, fasta, fasta_fai, dict )
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}
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