mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
9767b081b9
* feat: merge freebayes subtools * fix: typo * assess comments from review * fix: path to module
95 lines
4.4 KiB
Text
95 lines
4.4 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { FREEBAYES } from '../../../modules/freebayes/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_freebayes {
|
|
|
|
input = [ [ id:'test', single_end:false ], // 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),
|
|
[],
|
|
[]
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
targets = []
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_bed {
|
|
|
|
input = [ [ id:'test', single_end:false ], // 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),
|
|
[],
|
|
[]
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_cram {
|
|
|
|
input = [ [ id:'test', single_end:false ], // 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),
|
|
[],
|
|
[]
|
|
]
|
|
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)
|
|
targets = []
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_somatic {
|
|
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], 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)
|
|
targets = []
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_somatic_cram_intervals {
|
|
|
|
input = [ [ id:'test', single_end:false ], // 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']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], 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)
|
|
targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
|
}
|