mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
be8d7b3293
* Rollback version * Start work rollback to 0.4.1 * Further changes * Re do dynamic flag creation * Prettier.
26 lines
981 B
Text
26 lines
981 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { UNZIP } from '../../../../modules/unzip/main.nf'
|
|
include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
|
|
include { MALT_RUN } from '../../../../modules/malt/run/main.nf'
|
|
|
|
workflow test_malt_run {
|
|
|
|
fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
seq_type = "DNA"
|
|
map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
|
|
mapping_type = 'ref'
|
|
mapping_db = 'taxonomy'
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
|
|
]
|
|
mode = "BlastN"
|
|
|
|
UNZIP ( map_accession )
|
|
MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
|
|
MALT_RUN ( input, mode, MALT_BUILD.out.index )
|
|
}
|
|
|