mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
22 lines
1.2 KiB
Text
22 lines
1.2 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { UNTAR } from '../../../../software/untar/main.nf'
|
||
|
|
include { ARTIC_MINION } from '../../../../software/artic/minion/main.nf' addParams( fast5_dir: true, sequencing_summary: true, artic_minion_medaka_model:false )
|
||
|
|
|
||
|
|
workflow test_artic_minion {
|
||
|
|
|
||
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
|
||
|
|
fast5_tar = [ file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
|
||
|
|
sequencing_summary = [ file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true) ]
|
||
|
|
fasta = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true) ]
|
||
|
|
bed = [ file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true) ]
|
||
|
|
dummy_file = [ ]
|
||
|
|
|
||
|
|
fast5_dir = UNTAR ( fast5_tar ).untar
|
||
|
|
|
||
|
|
ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, dummy_file, 'nCoV-2019', '3')
|
||
|
|
}
|