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https://github.com/MillironX/nf-core_modules.git
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65 lines
2.6 KiB
Text
65 lines
2.6 KiB
Text
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#!/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' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
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include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn --method wgs' ] )
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include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf' addParams( options: [ 'args': '--method wgs' ] )
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workflow test_cnvkit_hybrid {
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tumor = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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tumor,
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normal
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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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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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normal
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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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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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normal = file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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normal
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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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tumor = file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test'], // meta map
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tumor,
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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, [], [], reference )
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}
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