mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
f5d5926516
* Match target bed to input files * Intervals in getpileupsumamries * more interval updates * change targets in strelka * remove leftover channel * fix checksums * add new test vcfs * add new test vcfs * Update modules/freebayes/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
102 lines
4.4 KiB
Text
102 lines
4.4 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { FREEBAYES } from '../../../modules/freebayes/main.nf'
|
|
|
|
workflow test_freebayes {
|
|
targets = []
|
|
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),
|
|
[],
|
|
[],
|
|
targets
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_bed {
|
|
|
|
targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
|
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),
|
|
[],
|
|
[],
|
|
targets
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_cram {
|
|
|
|
targets = []
|
|
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),
|
|
[],
|
|
[],
|
|
targets
|
|
]
|
|
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)
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_somatic {
|
|
|
|
targets = []
|
|
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),
|
|
targets
|
|
]
|
|
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)
|
|
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
|
}
|
|
|
|
workflow test_freebayes_somatic_cram_intervals {
|
|
|
|
targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
|
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),
|
|
targets
|
|
]
|
|
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)
|
|
samples = []
|
|
populations = []
|
|
cnv = []
|
|
|
|
FREEBAYES (input, fasta, fai, samples, populations, cnv)
|
|
}
|