mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
33 lines
1.6 KiB
Text
33 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
|
|
include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
|
|
|
|
|
|
workflow test_gatk_indelrealigner {
|
|
|
|
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
|
|
|
input_realignertargetcreator = [ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
]
|
|
|
|
GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )
|
|
|
|
ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals
|
|
|
|
ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
|
|
])
|
|
|
|
ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")
|
|
|
|
GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
|
|
}
|