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33 lines
1.6 KiB
Text
33 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
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include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
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workflow test_gatk_indelrealigner {
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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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input_realignertargetcreator = [ [ 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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GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
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ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
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ch_bams_indelrealigner = 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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ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
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GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
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}
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