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17fbdf96cb
* Adding tar.gz kraken2 db to test data * Update test path files for untar module * Update test path files for kraken2/run module * Update test path files for cat/fastq module
24 lines
931 B
Text
24 lines
931 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { KRAKEN2_RUN } from '../../../../software/kraken2/run/main.nf' addParams( options: [:] )
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workflow test_kraken2_run_single_end {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
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]
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db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
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KRAKEN2_RUN ( input, db )
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}
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workflow test_kraken2_run_paired_end {
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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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db = file(params.test_data['sarscov2']['genome']['kraken2'], checkIfExists: true)
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KRAKEN2_RUN ( input, db )
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}
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