nf-core_modules/tests/software/ivar/variants/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
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include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
workflow test_ivar_variants_no_gff_no_mpileup {
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params.gff = false
params.save_mpileup = false
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
def input = []
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input = [ [ id:'test'],
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file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, dummy )
}
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workflow test_ivar_variants_no_gff_with_mpileup {
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params.gff = false
params.save_mpileup = true
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
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def input = []
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input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, dummy )
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}
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workflow test_ivar_variants_with_gff_with_mpileup {
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params.gff = true
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params.save_mpileup = true
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def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
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def gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
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def input = []
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input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, gff )
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}