Removed errors.

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 +43,11 @@ onerror:
 rule all:
     """Define desired output from pipeline."""
     input:
+        "GO/comparison.txt",
         "Settings/Report.txt",
         #"Samplesize/Report.txt",
         #"Reports/Tools.txt",
-        "GO/comparison.txt"
-#        "Samplesize/Report.txt"
+        #"Samplesize/Report.txt"
 
 rule help:
     """Print list of all targets with help."""

config.yaml

 #Directories to be specified
-#workdir: /home/bftan/CNA_results        #directory to write output
-#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
+workdir: /home/bftan/CNA_results        #directory to write output
+gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
 
-#workdir: /home/bftan/CNA_results        #directory to write output
-#gisticdir: /home/bftan/Tools/GISTIC2    #directory to install GISTIC2
-
-workdir: /home/beatrice/CNA_analysis
-gisticdir: /home/beatrice/CNA_analysis/run_gistic2
+#workdir: /home/beatrice/CNA_analysis
+#gisticdir: /home/beatrice/CNA_analysis/run_gistic2
 
 #Input details to download from firehose
 cancer_type: SKCM

rules/ComparisonSettings.smk

+import os.path
+
 rule gistic_settings:
     """Run GISTIC2 based on different settings."""
     input:
         gistic_directory=os.path.join(config["gisticdir"], "gistic2"),
         seg="Input/Segments_tumor.txt"
     output:
-        expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"])),
-        expand("Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed", setting_nr=range(len(config["comparison_settings"]))
+        expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"]))),
+        expand("Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed", setting_nr=range(len(config["comparison_settings"])))
     params:
         cnv="",
         ref=config["reference"],
         ref_file="",
-        extra=config["comparison_settings"][{setting_nr}]
+        extra=expand("{setting}", setting=config["comparison_settings"])
     wrapper:
         "file:" + workflow.basedir + "/wrappers/GISTIC2"