Merged.

config_laptop.yaml

+#Directories to be specified
+#workdir: /home/bftan/CNA_results        #directory to write output
+#gisticdir: /home/bftan/Tools/GISTIC2_test    #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
+
+#Input details to download from firehose
+cancer_type: SKCM
+date_data: "2016_07_15"
+
+#Or provide input file
+inputfile: ""   #tumor segmentation data
+normal: ""      #normal segmentation data
+
+#Data for running and benchmarking tools.
+reference: hg19
+prev_found_genes: input_files/intogen-CM-drivers-data.tsv
+census_genes: input_files/Census_genes.txt
+biomart_genes: input_files/biomart_human_genes.tsv
+
+#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 for sample size differences
+sizes: [20, 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]