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Update main.nf

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Harshil Patel 2021-02-16 23:06:26 +00:00 committed by GitHub
parent 7c276d2974
commit cf2f0762aa
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1 changed files with 9 additions and 9 deletions
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18
tests/software/ivar/variants/main.nf
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@ -4,10 +4,10 @@ nextflow.enable.dsl = 2
include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:]) include { IVAR_VARIANTS } from '../../../../software/ivar/variants/main.nf' addParams([:])
params.gff = false
params.save_mpileup = false
workflow test_ivar_variants_no_gff_no_mpileup { workflow test_ivar_variants_no_gff_no_mpileup {
params.gff = false
params.save_mpileup = false
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true) def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
def input = [] def input = []
@ -16,10 +16,10 @@ workflow test_ivar_variants_no_gff_no_mpileup {
IVAR_VARIANTS ( input, ref, dummy ) IVAR_VARIANTS ( input, ref, dummy )
} }
params.gff = false
params.save_mpileup = true
workflow test_ivar_variants_no_gff_with_mpileup { workflow test_ivar_variants_no_gff_with_mpileup {
params.gff = false
params.save_mpileup = true
def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true) def ref = file("${launchDir}/tests/data/fasta/sarscov2/MN908947.3.fa", checkIfExists: true)
def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true) def dummy = file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true)
def input = [] def input = []
@ -28,10 +28,10 @@ workflow test_ivar_variants_no_gff_with_mpileup {
IVAR_VARIANTS ( input, ref, dummy ) IVAR_VARIANTS ( input, ref, dummy )
} }
params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
workflow test_ivar_variants_with_gff_with_mpileup { workflow test_ivar_variants_with_gff_with_mpileup {
params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3"
params.save_mpileup = true
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 gff = file(params.gff, checkIfExists: true)
def input = [] def input = []