From 8a27c35dd14aa76ca9171d49761205aabca34326 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Fri, 22 Nov 2024 13:30:10 -0500 Subject: [PATCH] fix: combinefilter reference --- modules/local/combinefilter.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/local/combinefilter.nf b/modules/local/combinefilter.nf index 2159dd5..b6fc6ce 100644 --- a/modules/local/combinefilter.nf +++ b/modules/local/combinefilter.nf @@ -2,7 +2,6 @@ GENOMEREF=file(params.genomes[params.genome].genome) GENOMEFAI=file(params.genomes[params.genome].genomefai) GENOMEDICT=file(params.genomes[params.genome].genomedict) -GERMLINE_RESOURCE=file(params.genomes[params.genome].germline_resource) process combineVariants { @@ -81,7 +80,7 @@ process combineVariants_alternative { script: vcfin = vcfs.join(" ") samplist=sample.split('_vs_') - if (vc.contains("lofreq")) { + if (vc.contains("lofreq") | vc.contains('deepsomatic')) { samporder = samplist[0] }else if(samplist.size()>1){ samporder = samplist.join(",")