mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
9c386c5dd8
* feat: add template for Bracken * chore: update version * refactor: change command build * refactor: rename report variable, change quotes * docs: remove refactored input parameter * fix: correctly assign arguments to options * tests: set up single and paired end tests * style: apply prettier * chore: change data sources to official ones * refactor: rename test workflows * tests: use correct input to the new UNTAR module * chore: update md5sums
57 lines
2.5 KiB
Text
57 lines
2.5 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'
|
|
include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
|
|
|
|
workflow test_bracken_bracken_single_end_default_args {
|
|
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_bracken_tar_gz'], checkIfExists: true)
|
|
|
|
ch_db = UNTAR ( [[:], db] ).untar
|
|
.map { it[1] }
|
|
KRAKEN2_KRAKEN2 ( input, ch_db )
|
|
BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
|
|
}
|
|
|
|
workflow test_bracken_bracken_single_end_custom_args {
|
|
input = [ [ id:'test', single_end:true, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
db = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
|
|
|
|
ch_db = UNTAR ( [[:], db] ).untar
|
|
.map { it[1] }
|
|
KRAKEN2_KRAKEN2 ( input, ch_db )
|
|
BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
|
|
}
|
|
|
|
workflow test_bracken_bracken_paired_end_default_args {
|
|
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_bracken_tar_gz'], checkIfExists: true)
|
|
|
|
ch_db = UNTAR ( [[:], db] ).untar
|
|
.map { it[1] }
|
|
KRAKEN2_KRAKEN2 ( input, ch_db )
|
|
BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
|
|
}
|
|
|
|
workflow test_bracken_bracken_paired_end_custom_args {
|
|
input = [ [ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], // 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_bracken_tar_gz'], checkIfExists: true)
|
|
|
|
ch_db = UNTAR ( [[:], db] ).untar
|
|
.map { it[1] }
|
|
KRAKEN2_KRAKEN2 ( input, ch_db )
|
|
BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
|
|
}
|