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https://github.com/MillironX/nf-core_modules.git
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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
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nextflow.enable.dsl = 2
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include { SHOVILL } from '../../../software/shovill/main.nf' addParams( options: [args: '--gsize 2800000 --kmers 31'] )
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include { SHOVILL as SHOVILL_SKESA } from '../../../software/shovill/main.nf' addParams( options: [args: '--assembler skesa --gsize 2800000'] )
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include { SHOVILL as SHOVILL_MEGAHIT } from '../../../software/shovill/main.nf' addParams( options: [args: '--assembler megahit --gsize 2800000'] )
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include { SHOVILL as SHOVILL_VELVET } from '../../../software/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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