nf-core_modules/tests/software/bowtie2/align/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
2021-02-03 16:20:02 +00:00
include { BOWTIE2_BUILD } from '../../../../software/bowtie2/build/main.nf' addParams( options: [:] )
include { BOWTIE2_ALIGN } from '../../../../software/bowtie2/align/main.nf' addParams( options: [:] )
workflow test_bowtie2_align_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}
workflow test_bowtie2_align_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) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index )
}