From 73ae3c3763fbf05f2090c93d24125cbb38651b43 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Fri, 21 Sep 2018 09:18:07 +0200
Subject: [PATCH] Use local normalization script
---
Snake.config.json | 1 -
Snakefile | 4 +---
2 files changed, 1 insertion(+), 4 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 89ed2b4..5091f09 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -4,7 +4,6 @@
"reference" : "/MMCI/TM/scratch/ref/GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna",
"mosaicatcher" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/build/mosaic",
"plot_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/qc.R",
- "norm_script" : "/MMCI/TM/scratch/strandseq/mosaicatcher-builds/v0.3/R/norm.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
diff --git a/Snakefile b/Snakefile
index 810e59a..3c35f68 100644
--- a/Snakefile
+++ b/Snakefile
@@ -436,11 +436,9 @@ rule normalize_counts:
"counts/{sample}/{window}_fixed_norm.txt.gz"
log:
"log/normalize_counts/{sample}/{window}_fixed.log"
- params:
- r_command = config["norm_script"]
shell:
"""
- Rscript {params.r_command} {input.counts} {input.norm} {output} 2>&1 > {log}
+ Rscript utils/normalize.R {input.counts} {input.norm} {output} 2>&1 > {log}
"""
rule link_normalized_info_file:
--
GitLab