fixes

Clinical-Genomics · Nov 21, 2024 · 0bf6a27 · 0bf6a27
1 parent 870820b
commit 0bf6a27
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/BALSAMIC/assets/scripts/merge_snv_variantcallers.py b/BALSAMIC/assets/scripts/merge_snv_variantcallers.py
@@ -252,11 +252,7 @@ def write_merged_vcf(output_file, header, merged_variants):
     """
     Writes the merged variants along with the header to the output VCF file.
     """
-    with (
-        gzip.open(output_file, "wt")
-        if output_file.endswith(".gz")
-        else open(output_file, "w")
-    ) as f:
+    with open(output_file, "w") as f:
         # Write the header
         for line in header:
             f.write(line + "\n")

diff --git a/BALSAMIC/snakemake_rules/variant_calling/merge_snv_vcfs.rule b/BALSAMIC/snakemake_rules/variant_calling/merge_snv_vcfs.rule
@@ -35,12 +35,15 @@ rule merge_snv_vcfs:
         Path(singularity_image, config["bioinfo_tools"].get("bcftools") + ".sif").as_posix()
     params:
         modify_tnscope_infofield = get_script_path("merge_snv_variantcallers.py"),
+        tmpdir = tempfile.mkdtemp(prefix=tmp_dir),
     threads:
         get_threads(cluster_config, "bcftools_concatenate_vcfs")
     message:
         "Merging VCFs with custom python script using vcfpy"
     shell:
         """
-python {params.modify_tnscope_infofield} {input.vcfs} {output.vcf_merged} ;
+python {params.modify_tnscope_infofield} {input.vcfs} {params.tmpdir}/merged.vcf ;
+bgzip {params.tmpdir}/merged.vcf ;
+mv {params.tmpdir}/merged.vcf {output.vcf_merged} ;
 tabix -p vcf -f {output.vcf_merged} ;
       """