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Fix tests to work with gff param

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Anders Goncalves da Silva 2021-02-15 11:51:04 -08:00
parent e8d1171b5d
commit 9a5aa0f145
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1 changed files with 5 additions and 4 deletions
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9
tests/software/ivar/variants/main.nf
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@ -8,18 +8,19 @@ include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addP
workflow test_ivar_variants_no_gff { workflow test_ivar_variants_no_gff {
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def gff = file('NO_FILE')
def input = [] def input = []
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ] file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, gff ) IVAR_VARIANTS ( input, ref )
} }
params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
workflow test_ivar_variants_with_gff { workflow test_ivar_variants_with_gff {
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
def input = [] def input = []
input = [ [ id:'test'], input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ] file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, gff ) IVAR_VARIANTS ( input, ref )
} }