fixes

Hoohm · Feb 5, 2017 · 5234b1f · 5234b1f
1 parent efb80a4
commit 5234b1f
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Showing 2 changed files with 11 additions and 6 deletions.
diff --git a/Rscripts/knee_plot.R b/Rscripts/knee_plot.R
@@ -1,5 +1,6 @@
 library(jsonlite)
 args = commandArgs(TRUE)
+path = args[1]
 
 # You can tweak here the fraction of reads you expect
 # when a cell is captured. I've found that this value often
@@ -9,7 +10,6 @@ fraction = 0.001
 #You can tweak the multiplier of barcodes you need here
 # to change the value on the X axis
 xlim = 2.5 * fromJSON(paste0(path,'/config.json'))$Barcodes
-path = args[1]
 
 samples = names(fromJSON(paste0(path,'/config.json'))$Samples)
 

diff --git a/dropseq.py b/dropseq.py
@@ -1,6 +1,7 @@
 import subprocess
 import sys
 import os
+import json
 
 try:
 	sys.argv[1]
@@ -9,6 +10,7 @@
 	exit()
 wrkdir = sys.argv[1]
 configfile = os.path.join(wrkdir, 'config.json')
+local_config_file = 'local.json'
 FOLDERS = ['summary', 'logs', 'plots']
 
 if (not os.path.isfile(configfile)):
@@ -18,12 +20,15 @@
 	joined = os.path.join(wrkdir, folder)
 	if(not os.path.isdir(joined)):
 		os.mkdir(joined)
-
+
+with open(local_config_file) as config_json:
+    json_data = json.load(config_json)
+
 #Optimized Run for dropseq
-first = 'snakemake -s snakefiles/Dropseq_pre_align.snake --cores 6 -pT -d {} --configfile local.json'.format(sys.argv[1])
-second = 'snakemake -s snakefiles/Star_align.snake --cores 6 -pT -d {} --configfile local.json'.format(sys.argv[1])
-third = 'snakemake -s snakefiles/Dropseq_post_align.snake --cores 6 -pT -d {} --configfile local.json'.format(sys.argv[1])
-knee_plot = 'Rscript ../Rscripts/knee_plot.R {}'.format(sys.argv[1])
+first = 'snakemake -s snakefiles/Dropseq_pre_align.snake --cores {} -pT -d {} --configfile local.json'.format(json_data['CORES'], sys.argv[1])
+second = 'snakemake -s snakefiles/Star_align.snake --cores {} -pT -d {} --configfile local.json'.format(json_data['CORES'], sys.argv[1])
+third = 'snakemake -s snakefiles/Dropseq_post_align.snake --cores {} -pT -d {} --configfile local.json'.format(json_data['CORES'], sys.argv[1])
+knee_plot = 'Rscript Rscripts/knee_plot.R {}'.format(sys.argv[1])
 print('Running pre_processing')
 subprocess.call(first, shell=True)
 print('Running Alignement')