mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
48 lines
2.7 KiB
Text
48 lines
2.7 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_APPLYBQSR_SPARK } from '../../../../modules/gatk4/applybqsrspark/main.nf'
|
||
|
|
|
||
|
|
workflow test_gatk4_applybqsr_spark {
|
||
|
|
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_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
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)
|
||
|
|
|
||
|
|
GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_applybqsr_spark_intervals {
|
||
|
|
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_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
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)
|
||
|
|
|
||
|
|
GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_applybqsr_spark_cram {
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_APPLYBQSR_SPARK ( input, fasta, fai, dict )
|
||
|
|
}
|