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24 lines
917 B
Text
24 lines
917 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MANTA_CONVERTINVERSION } from '../../../../modules/manta/convertinversion/main.nf'
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include { MANTA_TUMORONLY } from '../../../../modules/manta/tumoronly/main.nf'
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workflow test_manta_convertinversion {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
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[], []
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
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MANTA_TUMORONLY ( input, fasta, fai )
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MANTA_CONVERTINVERSION ( MANTA_TUMORONLY.out.tumor_sv_vcf, fasta )
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}
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