mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
39 lines
1.7 KiB
Text
39 lines
1.7 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
|
||
|
|
include { BISCUIT_PILEUP } from '../../../../modules/biscuit/pileup/main.nf'
|
||
|
|
|
||
|
|
workflow test_biscuit_pileup {
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // meta map
|
||
|
|
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_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_bai'], checkIfExists: true)],
|
||
|
|
[], //tumor bam
|
||
|
|
[] //tumor bai
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
BISCUIT_INDEX ( fasta )
|
||
|
|
BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_biscuit_pileup_somatic {
|
||
|
|
|
||
|
|
input = [ [ id:'test' ], // 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)
|
||
|
|
|
||
|
|
BISCUIT_INDEX ( fasta )
|
||
|
|
BISCUIT_PILEUP ( input, BISCUIT_INDEX.out.index )
|
||
|
|
|
||
|
|
}
|