nf-core_modules/tests/modules/kaiju/kaiju/main.nf
2022-04-13 14:53:08 +02:00

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Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
workflow test_kaiju_kaiju_single_end {
input = [
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
UNTAR ( db )
KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
}
workflow test_kaiju_kaiju_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) ]
]
db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
UNTAR ( db )
KAIJU_KAIJU ( input, UNTAR.out.untar.map{ it[1] } )
}