mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
47 lines
1.6 KiB
Text
47 lines
1.6 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
|
|
|
|
workflow test_ivar_variants_no_gff_no_mpileup {
|
|
|
|
input = [
|
|
[ id:'test'],
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
gff = []
|
|
save_mpileup = false
|
|
|
|
IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
|
|
}
|
|
|
|
workflow test_ivar_variants_no_gff_with_mpileup {
|
|
|
|
input = [
|
|
[ id:'test'],
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
gff = []
|
|
save_mpileup = true
|
|
|
|
IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
|
|
}
|
|
|
|
workflow test_ivar_variants_with_gff_with_mpileup {
|
|
|
|
input = [
|
|
[ id:'test'],
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
|
|
save_mpileup = true
|
|
|
|
IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
|
|
}
|