mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
49 lines
2 KiB
Text
49 lines
2 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { BISCUIT_INDEX } from '../../../../modules/biscuit/index/main.nf'
|
||
|
|
include { BISCUIT_EPIREAD } from '../../../../modules/biscuit/epiread/main.nf'
|
||
|
|
|
||
|
|
workflow test_biscuit_epiread_nosnp {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
[] //SNP BED file
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
BISCUIT_INDEX( fasta )
|
||
|
|
BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_biscuit_epiread_snp {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
BISCUIT_INDEX( fasta )
|
||
|
|
BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_biscuit_epiread_snp_decompress {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam_bai'], checkIfExists: true),
|
||
|
|
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
|
||
|
|
BISCUIT_INDEX( fasta )
|
||
|
|
BISCUIT_EPIREAD ( input, BISCUIT_INDEX.out.index )
|
||
|
|
}
|