Commit 063e5890 authored by BeatriceTan's avatar BeatriceTan
Browse files
parents 82ca2106 aebc3574
...@@ -42,8 +42,8 @@ onerror: ...@@ -42,8 +42,8 @@ onerror:
rule all: rule all:
"""Define desired output from pipeline.""" """Define desired output from pipeline."""
input: input:
#"Samplesize/Report.txt", "Samplesize/Report.txt",
"Reports/Tools.txt", #"Reports/Tools.txt",
#"Reports/Overlap_regions.bed" #"Reports/Overlap_regions.bed"
#"Reports/Segments.txt", #"Reports/Segments.txt",
#"GO/comparison.txt" #"GO/comparison.txt"
......
#Directories to be specified #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 gisticdir: /home/bftan/Tools/GISTIC2 #directory to install GISTIC2
#workdir: /home/beatrice/CNA_analysis #workdir: /home/beatrice/CNA_analysis
...@@ -31,6 +31,6 @@ settings_gistic: "-ta 0.1 ...@@ -31,6 +31,6 @@ settings_gistic: "-ta 0.1
-conf 0.99" -conf 0.99"
#Settings for sample size differences #Settings for sample size differences
#sizes: [20, 30, 40, 50, 60, 70, 80, 90] #sizes: [30, 40, 50, 60, 70, 80, 90]
sizes: [20] sizes: [30, 40]
repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] 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: ...@@ -13,7 +13,8 @@ rule run_gistic:
gistic_directory=config["gisticdir"], gistic_directory=config["gisticdir"],
seg="Input/Segments_tumor.txt" seg="Input/Segments_tumor.txt"
output: 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: params:
cnv="", cnv="",
ref=config["reference"], ref=config["reference"],
......
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