mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
32 lines
1.8 KiB
Text
32 lines
1.8 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_APPLYBQSR } from '../../../../software/gatk4/applybqsr/main.nf' addParams( options: [:] )
|
|
|
|
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)
|
|
]
|
|
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)
|
|
intervals = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
|
|
|
GATK4_APPLYBQSR ( input, fasta, fai, dict, intervals )
|
|
}
|