Commit aebc3574 authored by Tan's avatar Tan

Updated for cluster and fixed bed rule dependency.

parent 2defc593
......@@ -42,8 +42,8 @@ onerror:
rule all:
"""Define desired output from pipeline."""
input:
#"Samplesize/Report.txt",
"Reports/Tools.txt",
"Samplesize/Report.txt",
#"Reports/Tools.txt",
#"Reports/Overlap_regions.bed"
#"Reports/Segments.txt",
#"GO/comparison.txt"
......
#Directories to be specified
workdir: /home/bftan/CNA_results #directory to write output
workdir: /home/bftan/CNA_results2 #directory to write output
gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
#workdir: /home/beatrice/CNA_analysis
......@@ -31,6 +31,6 @@ settings_gistic: "-ta 0.1
-conf 0.99"
#Settings for sample size differences
sizes: [30, 40, 50, 60, 70, 80, 90]
#sizes: [20]
#sizes: [30, 40, 50, 60, 70, 80, 90]
sizes: [30, 40]
repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]
......@@ -13,7 +13,8 @@ rule run_gistic:
gistic_directory=config["gisticdir"],
seg="Input/Segments_tumor.txt"
output:
"GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt"
"GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt",
"GISTIC/regions_track.conf_" + config["gistic_precision"] + ".bed"
params:
cnv="",
ref=config["reference"],
......
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