nf-core_modules/tests/software/shovill/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SHOVILL } from '../../../software/shovill/main.nf' addParams( options: [args: '--gsize 2800000 --kmers 31'] )
include { SHOVILL as SHOVILL_SKESA } from '../../../software/shovill/main.nf' addParams( options: [args: '--assembler skesa --gsize 2800000'] )
include { SHOVILL as SHOVILL_MEGAHIT } from '../../../software/shovill/main.nf' addParams( options: [args: '--assembler megahit --gsize 2800000'] )
include { SHOVILL as SHOVILL_VELVET } from '../../../software/shovill/main.nf' addParams( options: [args: '--assembler velvet --gsize 2800000'] )
workflow test_shovill {
input = [ [ id:'test', single_end:false ], // meta map
[ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
]
SHOVILL ( input )
}
workflow test_shovill_megahit {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
SHOVILL_MEGAHIT ( input )
}
workflow test_shovill_skesa {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
SHOVILL_SKESA ( input )
}
workflow test_shovill_velvet {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
SHOVILL_VELVET ( input )
}