Updated settings.

Snakefile

@@ -18,7 +18,6 @@ include: "rules/GenePrioritization.smk"
 include: "rules/ComparisonRegions.smk"
 include: "rules/Circos.smk"
 include: "rules/SampleSizes.smk"
-#include: "rules/UseControl.smk"
 include: "rules/ComparisonSettings.smk"
 
 #Directory to save all files.
@@ -45,8 +44,9 @@ rule all:
     """Define desired output from pipeline."""
     input:
         #"Settings/Report.txt",
-        "PipelineResults.html",
-        "ComparisonResults.html"
+        "Samplesize/Report.txt"
+        #"PipelineResults.html",
+        #"GO/comparison.txt",
 
 rule help:
     """Print list of all targets with help."""

config.yaml

@@ -2,7 +2,7 @@
 #workdir: /home/bftan/CNA_results        #directory to write output
 #gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
-workdir: /home/beatrice/CNA_99_genegistic
+workdir: /home/beatrice/CNA_analysis #CNA_99_genegistic
 gisticdir: /home/beatrice/CNA_analysis/run_gistic2
 
 #Input details to download from firehose
@@ -32,5 +32,5 @@ comparison_settings: ["-brlen 0.7 -genegistic 1",
                       "-brlen 0.7 -genegistic 0"]
 
 #Settings for sample size differences
-sizes: [20, 30, 40, 50, 60, 70, 80, 90, 100, 110]
+sizes: [20, 30, 40, 50, 60, 70, 80, 90]
 repeats: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]