mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
826a5603db
* Stage fastq for concat in subfolders in task workdir * Update main.nf * Update test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
49 lines
1.8 KiB
Text
49 lines
1.8 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { CAT_FASTQ } from '../../../../modules/cat/fastq/main.nf'
|
|
|
|
workflow test_cat_fastq_single_end {
|
|
input = [
|
|
[ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
CAT_FASTQ ( input )
|
|
}
|
|
|
|
workflow test_cat_fastq_paired_end {
|
|
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),
|
|
file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
CAT_FASTQ ( input )
|
|
}
|
|
|
|
workflow test_cat_fastq_single_end_same_name {
|
|
input = [
|
|
[ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
CAT_FASTQ ( input )
|
|
}
|
|
|
|
workflow test_cat_fastq_paired_end_same_name {
|
|
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),
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
CAT_FASTQ ( input )
|
|
}
|