mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
25 lines
809 B
Text
25 lines
809 B
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_FASTQTOSAM } from '../../../../software/gatk4/fastqtosam/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
workflow test_gatk4_fastqtosam_single_end {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
|
||
|
|
|
||
|
|
GATK4_FASTQTOSAM ( input )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_fastqtosam_paired_end {
|
||
|
|
|
||
|
|
def input = []
|
||
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
|
||
|
|
file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ]
|
||
|
|
|
||
|
|
GATK4_FASTQTOSAM ( input )
|
||
|
|
}
|