Updated wrappers.

wrappers/GISTIC2/wrapper.py

@@ -10,7 +10,7 @@ from snakemake.shell import shell
 segments = os.path.abspath(snakemake.input.seg)
 gistic_dir = os.path.abspath(snakemake.input.gistic_directory).split("/gistic2")[0]
 outfolder = os.path.abspath(snakemake.output[0]).split("all_lesions")[0]
-print(outfolder)
+
 #Select reference file
 ref = snakemake.params.get("ref", "")
 ref_file = snakemake.params.get("ref_file", "")
@@ -27,10 +27,11 @@ if cnv_file != "":
     cnv_arg = " --cnv " + cnv_file if os.stat(cnv_file).st_size != 0 else " "
 else:
     cnv_arg = " "
-print(cnv_arg)
 
 #Additional arguments
 extra = snakemake.params.get("extra", "")
+if snakemake.params.confidence != "":
+    extra += "-conf 0." + snakemake.params.confidence
 
 #Make output directory, go to gistic2 directory and run gistic2
 command = "./gistic2 -b " + outfolder + " -seg " + segments + " -refgene " + reference + cnv_arg + extra

wrappers/topgo/wrapper.R

@@ -43,7 +43,7 @@ resultWeight <- getSigGroups(GOdata, test.stat)
 allRes <- GenTable(GOdata, classic = resultFisher,
                    #KS = resultKS,
                    weight = resultWeight,
-                   orderBy = "weight", ranksOf = "classic", topNodes = 50)
+                   orderBy = "weight", ranksOf = "classic") #, topNodes = 50)
 print(allRes)
 write.table(allRes, file=snakemake@output[[1]], quote=FALSE, sep="\t", eol = "\n")