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https://github.com/MillironX/nf-core_modules.git
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abe025677c
* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional NB: this is a breaking change, because the output channels have been renamed as a consequence of changes * updated yml * pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved * updated test yaml file for kraken2 * fixed TODOs and renamed variables and outputs * untar in conda cannot keep same md5sum of version, and therefore md5sum check removed * improved description of the options Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
37 lines
1.5 KiB
Text
37 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { UNTAR } from '../../../../modules/untar/main.nf'
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include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
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workflow test_kraken2_kraken2_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_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
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}
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workflow test_kraken2_kraken2_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_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
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}
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workflow test_kraken2_kraken2_classifyreads {
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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_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, true )
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}
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