Updated settings and all input.

Snakefile

@@ -17,6 +17,7 @@ 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.
 workdir: config["workdir"]
@@ -42,11 +43,13 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
-        "Settings/Report.txt",
+        #"Samplesize/Precision_recall.png"
+        #"Reports/Overlap_plots/NUP107.png"
+        #"Settings/Report.txt",
         #"Samplesize/Report.txt",
-        #"Reports/Tools.txt",
+        "Reports/Tools.txt",
+        "Reports/Circos/RecurrentRegions.png",
         "GO/comparison.txt"
-#        "Samplesize/Report.txt"
 
 rule help:
     """Print list of all targets with help."""

config.yaml

@@ -25,14 +25,7 @@ ID_to_GO: input_files/ID_to_GO.txt
 
 #Settings GISTIC2.0
 gistic_precision: "99"
-settings_gistic: "-ta 0.1
-                  -td 0.1
-                  -qvt 0.25
-                  -brlen 0.7
-                  -cap 1.5
-                  -rx 1
-                  -genegistic 1
-                  -conf 0.99"
+settings_gistic: ""
 
 comparison_settings: ["-ta 0.1 -td 0.1 -qvt 0.25 -brlen 0.7 -cap 1.5 -rx 1 -genegistic 1 -conf 0.99",
                       "-ta 0.1 -td 0.1 -qvt 0.25 -brlen 0.7 -cap 1.5 -rx 1 -genegistic 1 -conf 0.75",