From 76d93a8da5124c7a8e3434a5583cfc7f2ef3e94b Mon Sep 17 00:00:00 2001 From: EladH1 Date: Fri, 17 Jan 2025 10:57:51 +0100 Subject: [PATCH] fix small test relative path --- workflows/variantbenchmarking.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/variantbenchmarking.nf b/workflows/variantbenchmarking.nf index 0d6ee56..5714c78 100644 --- a/workflows/variantbenchmarking.nf +++ b/workflows/variantbenchmarking.nf @@ -81,11 +81,11 @@ workflow VARIANTBENCHMARKING { }else{ if (params.genome == "GRCh38"){ - rename_chr = Channel.fromPath("assets/rename_contigs/grch37_grch38.txt", checkIfExists: true).map{ txt -> tuple([id: txt.getSimpleName()], txt) }.collect() + rename_chr = Channel.fromPath("${projectDir}/assets/rename_contigs/grch37_grch38.txt", checkIfExists: true).map{ txt -> tuple([id: txt.getSimpleName()], txt) }.collect() } else if(params.genome == "GRCh37") { - rename_chr = Channel.fromPath("assets/rename_contigs/grch38_grch37.txt", checkIfExists: true).map{ txt -> tuple([id: txt.getSimpleName()], txt) }.collect() + rename_chr = Channel.fromPath("${projectDir}/assets/rename_contigs/grch38_grch37.txt", checkIfExists: true).map{ txt -> tuple([id: txt.getSimpleName()], txt) }.collect() } else{ rename_chr = Channel.empty()