nf-core_modules/tests/modules/ivar/variants/main.nf
Harshil Patel b4c6b430d0
Remove params call in ivar variants module (#1203)
* Remove params call in ivar variants module

* Update main.nf
2022-01-12 16:43:26 +00:00

44 lines
1.3 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)
gff = []
save_mpileup = false
IVAR_VARIANTS ( input, fasta, 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)
gff = []
save_mpileup = true
IVAR_VARIANTS ( input, fasta, 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)
gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
save_mpileup = true
IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
}