mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
34 lines
1.1 KiB
Text
34 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
|
|
include { TIDDIT_SV } from '../../../../modules/tiddit/sv/main.nf'
|
|
|
|
workflow test_tiddit_sv_bam {
|
|
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) ]
|
|
]
|
|
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
BWA_INDEX( fasta )
|
|
|
|
TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
|
|
}
|
|
|
|
workflow test_tiddit_sv_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) ]
|
|
]
|
|
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
BWA_INDEX( fasta )
|
|
|
|
TIDDIT_SV ( input, fasta, BWA_INDEX.out.index)
|
|
}
|