mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
14 lines
533 B
Text
14 lines
533 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
params.save_mpileup = true
|
|
include { IVAR_CONSENSUS } from '../../../../software/ivar/consensus/main.nf' addParams( [ options: [args2: '-aa -A -d 0 -Q 0'] ] )
|
|
|
|
workflow test_ivar_consensus {
|
|
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
|
|
def input = []
|
|
input = [ [ id:'test'],
|
|
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
|
|
IVAR_CONSENSUS ( input, ref )
|
|
}
|