mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-22 08:12:03 +00:00
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: ['args': '--rnaviral'] )
|
||
|
|
|
||
|
|
workflow test_spades_single_end {
|
||
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
coronaspades = false
|
||
|
|
|
||
|
|
SPADES ( input, [], coronaspades )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_spades_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) ]
|
||
|
|
]
|
||
|
|
coronaspades = false
|
||
|
|
|
||
|
|
SPADES ( input, [], coronaspades )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_coronospades_single_end {
|
||
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
coronaspades = true
|
||
|
|
|
||
|
|
SPADES ( input, [], coronaspades )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_coronospades_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) ]
|
||
|
|
]
|
||
|
|
coronaspades = true
|
||
|
|
|
||
|
|
SPADES ( input, [], coronaspades )
|
||
|
|
}
|
||
|
|
|