From 701849dbd0ad8ba352cb6a1c688f64426ac8eadf Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Wed, 10 Jan 2018 15:04:00 +0100
Subject: [PATCH] Made R reference (needed in Strand-PhaseR) a config parameter
---
Snake.config.json | 1 +
Snakefile | 3 +--
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 98afdad..53cd157 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -16,6 +16,7 @@
"50000" : "utils/variable_bins.GRCh38.50kb.bed",
"100000" : "utils/variable_bins.GRCh38.100kb.bed"
},
+ "R_reference" : "BSgenome.Hsapiens.UCSC.hg38",
"bp_density" : {
"few" : 0.1,
diff --git a/Snakefile b/Snakefile
index f4688c2..b29a56a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -11,7 +11,6 @@ BAM, = glob_wildcards("bam/{bam}.bam")
rule all:
input:
- "log/StrandPhaseR.config",
expand("plots/" + config["sample"] + ".{window}_fixed.pdf", window = [50000, 100000, 200000, 500000]),
expand("plots/" + config["sample"] + ".{window}_variable.pdf", window = [50000, 100000]),
expand("segmentation2/" + config["sample"] + ".{window}_fixed.{bpdens}.txt",
@@ -287,7 +286,7 @@ rule prepare_strandphaser_config_per_chrom:
print("compareSingleCells = TRUE", file = f)
print("callBreaks = FALSE", file = f)
print("exportVCF = '", config["sample"], ".txt'", sep = "", file = f)
- print("bsGenome = 'BSgenome.Hsapiens.UCSC.hg19'", file = f)
+ print("bsGenome = '", config["R_reference"], "'", file = f)
--
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