nf-core_modules/tests/modules/metaphlan3/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR } from '../../../modules/untar/main.nf' addParams( options: [:] )
include { SAMTOOLS_VIEW } from '../../../modules/samtools/view/main.nf' addParams( options: ['suffix': '.sam'] )
include { METAPHLAN3 } from '../../../modules/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 )
}