mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
60 lines
2.3 KiB
Text
60 lines
2.3 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { UNTAR } from '../../../software/untar/main.nf' addParams( options: [:] )
|
||
|
|
include { SAMTOOLS_VIEW } from '../../../software/samtools/view/main.nf' addParams( options: ['suffix': '.sam'] )
|
||
|
|
include { METAPHLAN3 } from '../../../software/metaphlan3/main.nf' addParams( options: [ 'args':'--index mpa_v30_CHOCOPhlAn_201901 --add_viruses --bt2_ps very-sensitive-local' ] )
|
||
|
|
|
||
|
|
workflow test_metaphlan3_single_end {
|
||
|
|
|
||
|
|
input = [ [ id:'test', single_end:true ], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
|
||
|
|
db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
|
||
|
|
|
||
|
|
UNTAR ( db )
|
||
|
|
METAPHLAN3 ( input, UNTAR.out.untar )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_metaphlan3_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 = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
|
||
|
|
|
||
|
|
|
||
|
|
UNTAR ( db )
|
||
|
|
METAPHLAN3 ( input, UNTAR.out.untar )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_metaphlan3_sam {
|
||
|
|
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
|
||
|
|
db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
|
||
|
|
|
||
|
|
|
||
|
|
UNTAR ( db )
|
||
|
|
SAMTOOLS_VIEW ( input )
|
||
|
|
METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_metaphlan3_fasta {
|
||
|
|
|
||
|
|
input = [ [ id:'test', single_end:true], // meta map
|
||
|
|
[ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
|
||
|
|
]
|
||
|
|
|
||
|
|
db = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
|
||
|
|
|
||
|
|
UNTAR ( db )
|
||
|
|
METAPHLAN3 ( input, UNTAR.out.untar )
|
||
|
|
}
|