Merge branch 'master' of https://gitlab.com/BeatriceTan/PrioritizationCNAs

Snakefile

@@ -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"

config.yaml

 #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: [20, 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]

rules/GISTIC2.smk

@@ -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"],