mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 21:53:10 +00:00
940d7fe9d6
* Move MetaPhlAn3 to a subcommand and add mergemetaphlantables * Add mergemetaphlantables tests * Add mergemetaphlantables to test config * Apply suggestions from code review * Revert now unnecessary input channel name change and now document * Update modules/metaphlan3/mergemetaphlantables/main.nf * Require database directory and more details in description
22 lines
1,010 B
Text
22 lines
1,010 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNTAR } from '../../../../modules/untar/main.nf'
|
|
include { METAPHLAN3 } from '../../../../modules/metaphlan3/metaphlan3/main.nf'
|
|
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../../../modules/metaphlan3/mergemetaphlantables/main.nf'
|
|
|
|
workflow test_metaphlan3_mergemetaphlantables {
|
|
|
|
input = Channel.of(
|
|
[[ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]],
|
|
[[ id:'test2', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]]
|
|
)
|
|
|
|
db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
|
|
|
|
UNTAR ( db )
|
|
METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
|
|
METAPHLAN3_MERGEMETAPHLANTABLES ( METAPHLAN3.out.profile.map{it[1]}.collect() )
|
|
|
|
}
|