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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
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nextflow.enable.dsl = 2
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include { SHOVILL } from '../../../modules/shovill/main.nf' addParams( options: [args: '--gsize 2800000 --kmers 31'] )
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include { SHOVILL as SHOVILL_SKESA } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler skesa --gsize 2800000'] )
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include { SHOVILL as SHOVILL_MEGAHIT } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler megahit --gsize 2800000'] )
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include { SHOVILL as SHOVILL_VELVET } from '../../../modules/shovill/main.nf' addParams( options: [args: '--assembler velvet --gsize 2800000'] )
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workflow test_shovill {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_1.fastq.gz", checkIfExists: true),
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file("https://github.com/nf-core/test-datasets/raw/bacass/ERR044595_1M_2.fastq.gz", checkIfExists: true) ]
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]
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SHOVILL ( input )
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}
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workflow test_shovill_megahit {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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SHOVILL_MEGAHIT ( input )
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}
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workflow test_shovill_skesa {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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SHOVILL_SKESA ( input )
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}
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workflow test_shovill_velvet {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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SHOVILL_VELVET ( input )
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}
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