From 07479b7007b5e0feb92e2fbe3ff2b1f580370513 Mon Sep 17 00:00:00 2001
From: maryamghr <maryam@lap-13-67.mmci.uni-saarland.de>
Date: Mon, 4 Dec 2017 13:47:02 +0100
Subject: [PATCH] removed class_dir & class_script params
---
Snake.config.json | 2 --
Snakefile | 2 --
2 files changed, 4 deletions(-)
diff --git a/Snake.config.json b/Snake.config.json
index 636c429..98afdad 100644
--- a/Snake.config.json
+++ b/Snake.config.json
@@ -9,8 +9,6 @@
"sce_script" : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/sce_utils/SCE.R",
"samtools" : "samtools",
"bcftools" : "bcftools",
- "class_script" : "finalCall_cmd.R",
- "class_dir" : "/g/korbel/meiers/tools/mosaicatcher/strandsequtils/maryamCode",
"exclude_file" : "/g/korbel/meiers/tools/mosaicatcher/mosaicatcher/data/exclude/hg19.exclude",
diff --git a/Snakefile b/Snakefile
index 820cc26..3723b7f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -159,8 +159,6 @@ rule run_sv_classification:
outdir = "sv_probabilities/" + config["sample"] + ".{windows}.{bpdens}/",
out1 = "sv_probabilities/" + config["sample"] + ".{windows}.{bpdens}/allSegCellProbs.table"
params:
- class_dir = config["class_dir"],
- class_command = "Rscript " + config["class_dir"] + "/" + config["class_script"],
windowsize = lambda wc: wc.windows.split("_")[0]
shell:
"""
--
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