From a79703fcf6e533e242a1565afe6ad62ae46b456f Mon Sep 17 00:00:00 2001 From: Danny Park Date: Wed, 11 Mar 2015 16:55:11 -0400 Subject: [PATCH] fix snakemake isnvs_vcf merge rule --- pipes/rules/intrahost.rules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/rules/intrahost.rules b/pipes/rules/intrahost.rules index 6dfd14d0e..78732e547 100644 --- a/pipes/rules/intrahost.rules +++ b/pipes/rules/intrahost.rules @@ -46,7 +46,7 @@ rule isnvs_vcf: run: shell("{config[binDir]}/intrahost.py merge_to_vcf {params.refGenome} {output[0]}" + " --samples {params.samples}" - + " --isnvs " + " ".join("{config[dataDir]}/{config[subdirs][intrahost]}/vphaser2."+s+".txt" for s in params.samples) + + " --isnvs " + " ".join("{config[dataDir]}/{config[subdirs][intrahost]}/vphaser2."+s+".txt.gz" for s in params.samples) + " --assemblies " + " ".join("{config[dataDir]}/{config[subdirs][assembly]}/"+s+".fasta" for s in params.samples) ) shell("{config[binDir]}/interhost.py snpEff {output[0]} {params.snpEff_ref} {output[1]} --strip_chr_version")