Fixed merge conflicts.

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

@@ -10,8 +10,8 @@ rule gistic_settings:
         seg="Input/Segments_tumor.txt",
         lambda wildcards: config["comparison_settings"][wildcards.setting]
     output:
-        "Settings/GISTIC_wildcards.setting/all_lesions.conf_" + config["gistic_precision"] + ".txt",
-        "Settings/GISTIC_wildcards.setting/regions_track.conf_" + config["gistic_precision"] + ".bed"
+        expand("Settings/GISTIC_{setting_nr}/all_lesions.conf_" + config["gistic_precision"] + ".txt", setting_nr=range(len(config["comparison_settings"]))),
+        "Settings/GISTIC_{setting_nr}/regions_track.conf_" + config["gistic_precision"] + ".bed"
     params:
         cnv="",
         ref=config["reference"],

rules/GenePrioritization.smk

@@ -3,7 +3,8 @@ rule do_GO_analysis:
     input:
         gene_list="Reports/Genes_{tool}.txt"
     output:
-        go="GO/{tool}.txt"
+        table="GO/Enriched_GOs_{tool}.txt",
+        plot="GO/Enriched_GOs_{tool}.jpg"
     params:
         organism="hsapiens",    #default is human
         ontology="BP",           #MF, BP, CC or all
@@ -16,7 +17,7 @@ rule do_GO_analysis:
 rule compare_enriched_GOs:
     """Compare the top 50 GO terms detected by RUBIC and GISTIC2.0"""
     input:
-        go=expand("GO/{tool}.txt", tool=["GISTIC2", "RUBIC"])
+        go=expand("GO/Enriched_GOs_{tool}.txt", tool=["GISTIC2", "RUBIC"])
     output:
         "GO/comparison.txt"
     run:

scripts/ReportTools.py

@@ -106,12 +106,13 @@ def venn3_overlap(gene_lists, known_genes, out_venn):
 def plot_histogram_sizes(parsed_results, plot_file):
     """Make boxplot with swarmplot on top showing sizes of recurrent regions detected by GISTIC2.0 and RUBIC."""
     size_list, size_list_known = parse_sizes_for_plot(parsed_results)
+    print(size_list_known)
     sns.set_style("white")
     f, ax = plt.subplots(figsize=(7, 7))
     ax.set(yscale="log")
     g = sns.boxplot(x="Tool", y="Size", hue="CNV type", data=size_list, whis=np.inf, palette={"Amplification": "#71AEC0", "Deletion": "#B55D60"})
     g = sns.swarmplot(x="Tool", y="Size", dodge=True, hue="CNV type", data=size_list, size=5, palette={"Amplification": "#527F8C", "Deletion": "#844446"})
-    g = sns.swarmplot(x="Tool", y="Size", dodge=True, hue="CNV type", data=size_list_known, size=5, palette={"Amplification": "black", "Deletion": "black"})
+    #g = sns.swarmplot(x="Tool", y="Size", dodge=True, hue="CNV type", data=size_list_known, size=5, palette={"Amplification": "black", "Deletion": "black"})
     sns.despine()
     g.set_xlabel("Tool",fontsize=16)
     g.set_ylabel("Log size of recurrent regions",fontsize=16)

wrappers/topgo/wrapper.R

@@ -48,5 +48,7 @@ print(allRes)
 write.table(allRes, file=snakemake@output[[1]], quote=FALSE, sep="\t", eol = "\n")
 
 #Visualize GO term relationships
+jpeg(snakemake@output[[1]])
 showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo ='all')
 printGraph(GOdata, resultFisher, firstSigNodes = 5, fn.prefix = "tGO", useInfo = "all", pdfSW = TRUE)
+dev.off()