CNV consensus (7 of 6): Remove duplicated coordinates and NULLs

analyses/copy_number_consensus_call/Snakefile

@@ -189,10 +189,21 @@ rule merge_all:
                           dupdel = ["dup", "del"])
     output:
         ## Define the final output file
-        "results/cnv_consensus.tsv"
+        "../../scratch/endpoints/all_CNVs_combined.tsv"
     shell:
         ## Add a header to the file and combine all of the files using cat. 
-       "echo -e 'chrom\tstart\tend\tmanta_CNVs\tcnvkit_CNVs\tfreec_CNVs\tCNV_type\tBiospecimen\tfile_names' "
+       "echo -e 'chrom\tstart\tend\tmanta_CNVs\tcnvkit_CNVs\tfreec_CNVs\tCNV_type\tsample\tfile_names' "
        " | cat - {input.bedfiles} "
        " | cut -f 1-8 "
        " > {output}"
+
+rule clean_output:
+    input:
+        script=os.path.join(config["scripts"], "remove_dup_NULL_entries.py"),
+        cnv_file ="../../scratch/endpoints/all_CNVs_combined.tsv"
+    output:
+        "results/cnv_consensus.tsv"
+    shell:
+        "python3 {input.script} --file {input.cnv_file} > {output}"
+
+