mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
44 lines
2 KiB
Text
44 lines
2 KiB
Text
#!/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 )
|
|
}
|