nf-core_modules/tests/modules/controlfreec/makegraph/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/controlfreec/makegraph/main.nf'
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_makegraph {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
CONTROLFREEC_MAKEGRAPH ( makegraph_in )
}
workflow test_controlfreec_makegraph_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
CONTROLFREEC_MAKEGRAPH ( makegraph_in )
}