mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
44 lines
1.1 KiB
Text
44 lines
1.1 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { PICARD_FASTQTOSAM } from '../../../../modules/picard/fastqtosam/main.nf'
|
||
|
|
|
||
|
|
workflow test_picard_fastqtosam_single {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:true ], // meta map
|
||
|
|
[
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
]
|
||
|
|
|
||
|
|
PICARD_FASTQTOSAM ( input )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_picard_fastqtosam_paired {
|
||
|
|
|
||
|
|
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)
|
||
|
|
]
|
||
|
|
]
|
||
|
|
|
||
|
|
PICARD_FASTQTOSAM ( input )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_picard_fastqtosam_paired_custom_samplename {
|
||
|
|
|
||
|
|
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)
|
||
|
|
]
|
||
|
|
]
|
||
|
|
|
||
|
|
PICARD_FASTQTOSAM ( input )
|
||
|
|
}
|