From cf2f0762aa44dc822634f11d9db6701b243a6c1e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 16 Feb 2021 23:06:26 +0000 Subject: [PATCH] Update main.nf --- tests/software/ivar/variants/main.nf | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/software/ivar/variants/main.nf b/tests/software/ivar/variants/main.nf index 07999457..306d4585 100644 --- a/tests/software/ivar/variants/main.nf +++ b/tests/software/ivar/variants/main.nf @@ -4,10 +4,10 @@ nextflow.enable.dsl = 2 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 { + 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 = [] @@ -16,10 +16,10 @@ workflow test_ivar_variants_no_gff_no_mpileup { IVAR_VARIANTS ( input, ref, dummy ) } -params.gff = false -params.save_mpileup = true - 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 = [] @@ -28,10 +28,10 @@ workflow test_ivar_variants_no_gff_with_mpileup { IVAR_VARIANTS ( input, ref, dummy ) } -params.gff = "${launchDir}/tests/data/gff/sarscov2/MN908947.3.gff3" - workflow test_ivar_variants_with_gff_with_mpileup { - + params.gff = "${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 gff = file(params.gff, checkIfExists: true) def input = []