removed class_dir & class_script params

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",

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:
         """