From 4538c902bb940cc33060b133a9e40f58822f1c87 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Thu, 11 Jan 2018 14:58:36 +0100
Subject: [PATCH] Fixing usage of wildcards
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 29aa7be..cde863a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -296,7 +296,7 @@ rule prepare_strandphaser_config_per_chrom:
with open(output[0], "w") as f:
print("[General]", file = f)
print("numCPU = 1", file = f)
- print("chromosomes = '{wildcards.chrom}'", file = f)
+ print("chromosomes = '" + wildcards.chrom + "'", file = f)
print("pairedEndReads = TRUE", file = f)
print("min.mapq = 10", file = f)
print("", file = f)
@@ -310,7 +310,7 @@ rule prepare_strandphaser_config_per_chrom:
print("splitPhasedReads = TRUE", file = f)
print("compareSingleCells = TRUE", file = f)
print("callBreaks = FALSE", file = f)
- print("exportVCF = '{sample}.txt'", sep = "", file = f)
+ print("exportVCF = '" + wildcards.sample + ".txt'", sep = "", file = f)
print("bsGenome = '", config["R_reference"], "'", sep = "", file = f)
--
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