nf-core_modules/tests/software/quast/main.nf
2021-02-01 13:13:21 +01:00

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Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { QUAST } from '../../../software/quast/main.nf' addParams(options: [:])
workflow test_quast_ref {
consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gff = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
def use_fasta = true
def use_gtf = true
QUAST( consensus, fasta, use_fasta, gff, use_gtf)
}
workflow test_quast_noref {
consensus = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gff = file('gff_dummy')
fasta = file('fasta_dummy')
def use_fasta = false
def use_gtf = false
QUAST( consensus, fasta, use_fasta, gff, use_gtf)
}