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69 lines
2.5 KiB
Text
Executable file
69 lines
2.5 KiB
Text
Executable file
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf'
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include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf'
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include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
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workflow test_cnvkit_hybrid {
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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_single_end_sorted_bam'], 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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targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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CNVKIT_HYBRID ( input, fasta, targets, [] )
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}
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workflow test_cnvkit_wgs {
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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_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], 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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CNVKIT_WGS ( input, fasta, [], [] )
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}
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workflow test_cnvkit_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']['test2_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], 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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CNVKIT_WGS ( input, fasta, [], [] )
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}
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workflow test_cnvkit_tumoronly {
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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_sorted_bam'], checkIfExists: true),
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[]
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]
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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, [], [], reference )
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}
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workflow test_cnvkit_tumoronly_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']['test2_paired_end_sorted_cram'], checkIfExists: true),
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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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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, fasta, [], reference )
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}
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