nf-core_modules/tests/modules/snapaligner/align/main.nf
2022-05-06 14:10:44 +02:00

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Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
workflow test_snapaligner_single {
input = [
[ id:'test', single_end:true ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
}
workflow test_snapaligner_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)]
]
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
}