mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
44 lines
2 KiB
Text
44 lines
2 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { SHOVILL } from '../../../modules/shovill/main.nf' addParams( options: [args: '--gsize 2800000 --kmers 31'] )
|
|
include { SHOVILL as SHOVILL_SKESA } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler skesa --gsize 2800000'] )
|
|
include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler megahit --gsize 2800000'] )
|
|
include { SHOVILL as SHOVILL_VELVET } from '../../../modules/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 )
|
|
}
|