nf-core_modules/tests/modules/cnvkit/batch/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
workflow test_cnvkit_hybrid_somatic {
input = [
[ id:'test' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
CNVKIT_HYBRID ( input, fasta, [], targets, [] )
}
workflow test_cnvkit_wgs_somatic {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, [], [], [] )
}
workflow test_cnvkit_cram_wgs_somatic {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
}
workflow test_cnvkit_tumoronly_hybrid_bam {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
[]
]
reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, [], [], [], reference )
}
workflow test_cnvkit_tumoronly_hybrid_cram {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
}
workflow test_cnvkit_germline_hybrid_cram {
input = [
[ id:'test'], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
CNVKIT_GERMLINE ( input, fasta, fasta_fai, targets, [])
}
workflow test_cnvkit_germline_hybrid_bam {
input = [
[ id:'test'], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
CNVKIT_GERMLINE ( input, fasta, [], targets, [])
}