mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 00:02:04 +00:00
043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
30 lines
1.1 KiB
Text
30 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
|
|
include { YARA_INDEX } from '../../../../software/yara/index/main.nf' addParams( options: ['args': '-e 3'] )
|
|
include { YARA_MAPPER } from '../../../../software/yara/mapper/main.nf' addParams( options: ['args': '-e 3'] )
|
|
|
|
workflow test_yara_single_end {
|
|
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
|
|
|
|
YARA_INDEX ( fasta )
|
|
YARA_MAPPER ( input, YARA_INDEX.out.index )
|
|
}
|
|
|
|
workflow test_yara_paired_end {
|
|
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] ]
|
|
|
|
YARA_INDEX ( fasta )
|
|
YARA_MAPPER ( input, YARA_INDEX.out.index )
|
|
}
|