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c99ab09f8d
* Add kraken2 pigz multi-tool container for compressing output fastq files * Add untar to pytest config * Add untar process to kraken2 tests * Remove unneeded tags
27 lines
1.1 KiB
Text
27 lines
1.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../software/untar/main.nf' addParams( options: [:] )
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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_tar_gz'], checkIfExists: true)
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UNTAR ( db )
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KRAKEN2_RUN ( input, UNTAR.out.untar )
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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_tar_gz'], checkIfExists: true)
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UNTAR ( db )
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KRAKEN2_RUN ( input, UNTAR.out.untar )
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}
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