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59 lines
2.2 KiB
Text
59 lines
2.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
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include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
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include { TIDDIT_SV as TIDDIT_SV_NOBWA } from '../../../../modules/tiddit/sv/main.nf'
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workflow test_tiddit_sv_bam {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX( fasta )
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TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
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}
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workflow test_tiddit_sv_cram {
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input = [
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[ id:'test' ], // 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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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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BWA_INDEX( fasta )
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TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
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}
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workflow test_tiddit_sv_nobwa_bam {
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input = [
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[ 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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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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TIDDIT_SV_NOBWA ( input, fasta, [])
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}
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workflow test_tiddit_sv_nobwa_cram {
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input = [
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[ id:'test' ], // 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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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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TIDDIT_SV_NOBWA ( input, fasta, [])
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}
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