nf-core_modules/tests/software/shovill/main.nf
Kevin Menden 043a7d1e3c
remove deprecated test tags (#440)
* remove deprecated test tags

* fix bowtie, gatk4/applybsqr

* fix gatk4 baserecalibrator

* fixed shovill

* fixed yara/mapper

* fixed kallistobustools/ref paths
2021-04-13 18:03:09 +01:00

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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(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
SHOVILL_MEGAHIT ( input )
}
workflow test_shovill_skesa {
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) ]
]
SHOVILL_SKESA ( input )
}
workflow test_shovill_velvet {
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) ]
]
SHOVILL_VELVET ( input )
}