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Add gff as input

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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Anders Goncalves da Silva 2021-02-15 19:54:19 -08:00 committed by GitHub
parent 4f8ab8bd69
commit 8b6989f2d7
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1 changed files with 3 additions and 2 deletions
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tests/software/ivar/variants/main.nf
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@ -19,8 +19,9 @@ params.gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkI
workflow test_ivar_variants_with_gff { workflow test_ivar_variants_with_gff {
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def gff = file(params.gff, checkIfExists: true)
def input = [] def input = []
input = [ [ id:'test'], input = [ [ id:'test'],
file("${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 ) IVAR_VARIANTS ( input, ref, gff )
} }