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Merge pull request #181 from drpatelh/fixes

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Fix tests for iVar variants
This commit is contained in:
Harshil Patel 2021-02-17 10:08:57 +00:00 committed by GitHub
commit 4d656c8f5f
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1 changed files with 7 additions and 7 deletions
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14
tests/software/ivar/variants/main.nf
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@ -7,11 +7,11 @@ include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addP
workflow test_ivar_variants_no_gff_no_mpileup {
params.gff = false
params.save_mpileup = false
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 = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, dummy )
}
@ -19,23 +19,23 @@ workflow test_ivar_variants_no_gff_no_mpileup {
workflow test_ivar_variants_no_gff_with_mpileup {
params.gff = false
params.save_mpileup = true
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, dummy )
}
workflow test_ivar_variants_with_gff_with_mpileup {
params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
params.gff = true
params.save_mpileup = true
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def gff = file(params.gff, checkIfExists: true)
def gff = file("${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3", checkIfExists: true)
def input = []
input = [ [ id:'test'],
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test-sc2-artic-v3-sorted-trimmed.bam", checkIfExists: true) ]
IVAR_VARIANTS ( input, ref, gff )
}