mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
a6e0629e24
* Change intervals to be part of sample specific input * Fix some tests * Update checksum * Update intervals * Update intervals * Try out gavins idea for adding the file * update test line * update test line * update test line * revert contains line
47 lines
2.6 KiB
Text
47 lines
2.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_APPLYBQSR } from '../../../../modules/gatk4/applybqsr/main.nf'
|
|
|
|
workflow test_gatk4_applybqsr {
|
|
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 ( input, fasta, fai, dict )
|
|
}
|
|
|
|
workflow test_gatk4_applybqsr_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 ( input, fasta, fai, dict )
|
|
}
|
|
|
|
workflow test_gatk4_applybqsr_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 ( input, fasta, fai, dict )
|
|
}
|