Restore previous code: fix has been done in svtyper

snakecnv/bin/svtyper_launcher.py

@@ -21,7 +21,7 @@ def input_is_empty(input_vcf):
     return is_empty
 
 
-def launch(bamlist, input_vcf, output_vcf, threads, chromosome):
+def launch(bamlist, input_vcf, output_vcf, threads):
     try:
         if input_is_empty(input_vcf):
             shutil.copy(input_vcf, output_vcf)
@@ -31,17 +31,14 @@ def launch(bamlist, input_vcf, output_vcf, threads, chromosome):
             else:
                 tabix_index(output_vcf)
         else:
-            vcf_out_dir = os.path.join(os.path.dirname(output_vcf), chromosome)
-            if not os.path.exists(vcf_out_dir):
-                os.mkdir(vcf_out_dir)
-            vcf_out = os.path.join(vcf_out_dir, os.path.basename(output_vcf[:-3]))
+            vcf_out = output_vcf[:-3]
             genotype_multiple_samples(bamlist=bamlist,
                                       vcf_in=input_vcf,
                                       vcf_out=vcf_out,
                                       cores=threads)
             if run("bcftools sort -O z -o {ovcf} {ivcf}".format(ivcf=vcf_out, ovcf=output_vcf), shell=True)\
                     .returncode == 0:
-                shutil.rmtree(vcf_out_dir)
+                os.remove(vcf_out)
                 tabix_index(output_vcf, force=True, preset="vcf")
             else:
                 print("Bctools sort command failed", file=sys.stderr)
@@ -67,8 +64,6 @@ if __name__ == "__main__":
                         help="Output VCF file")
     parser.add_argument("-t", "--threads", required=True, type=int,
                         help="Number of threads to use")
-    parser.add_argument("-c", "--chromosome", required=True, type=str,
-                        help="Chromosome name")
 
     args = parser.parse_args()
 

snakecnv/tools/genotyping.snk

@@ -21,7 +21,7 @@ rule svtyping:
         stderr = "{batch}/logs/svtyper/{chrom}_svtyper.e"
     shadow: "shallow"  # in order to prevent raw.vcf to be corrupted
     shell:
-        "svtyper_launcher.py -B {input.bamlist} -i {input.sites} -o {output.vcf} -t {threads} -c {wildcards.chrom} "
+        "svtyper_launcher.py -B {input.bamlist} -i {input.sites} -o {output.vcf} -t {threads} "
         " 1>{log.stdout} 2>{log.stderr}"
 
 rule genotyping: