Remove unused genotyping rule

snakecnv/tools/genotyping.snk

@@ -24,25 +24,3 @@ rule svtyping:
     shell:
         "svtyper_launcher.py -B {input.bamlist} -i {input.sites} -o {output.vcf} -t {threads} "
         " 1>{log.stdout} 2>{log.stderr}"
-
-rule genotyping:
-    input:
-        sites = "{batch}/merge/{chrom}/merge_{chrom}_{svtype}.vcf.gz",
-        bamlist = "{batch}/bamlist.list",
-        gendermap = "{batch}/genomestrip/gendermap.txt",
-        metadatadone = "{batch}/genomestrip/metadata/sample_gender.report.txt",
-        genome = REFERENCE
-    params:
-        metadata = "{batch}/genomestrip/metadata"
-    output:
-        "{batch}/genotypes/genomestrip_{chrom}_{svtype}_genotypes.vcf.gz"
-    threads:
-        get_threads("genotyping", 4)
-    log:
-        stdout = "{batch}/logs/genotyping/{chrom}_genomestrip.o",
-        stderr = "{batch}/logs/genotyping/{chrom}_genomestrip.e"
-    shell:
-        "gstrip_genotyper.sh {input.bamlist} {wildcards.chrom} {input.genome}"
-        " {params.metadata} genomestrip/{wildcards.chrom} {input.gendermap} "
-        " {input.sites} {output} {threads}"
-        " 1>{log.stdout} 2>{log.stderr}"