mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
|
include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
|
|
|
|
workflow test_kraken2_kraken2_single_end {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
|
|
|
|
UNTAR ( db )
|
|
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
|
|
}
|
|
|
|
workflow test_kraken2_kraken2_paired_end {
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
|
|
|
|
UNTAR ( db )
|
|
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, true, false )
|
|
}
|
|
|
|
workflow test_kraken2_kraken2_classifyreads {
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
db = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
|
|
|
|
UNTAR ( db )
|
|
KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, true )
|
|
}
|