remove temp file produced

jodyphelan · Dec 2, 2024 · 2223f50 · 2223f50
1 parent e7ed7cd
commit 2223f50
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/tbprofiler/consensus.py b/tbprofiler/consensus.py
@@ -71,6 +71,7 @@ def get_consensus_vcf(sample: str,input_vcf: str,args: argparse.Namespace) -> st
     run_cmd(f"cat {args.conf['ref']} {consensus_file}> {tmp_aln}")
     outfile = f"{args.files_prefix}.masked.vcf"
     run_cmd(f"fa2vcf.py {tmp_aln} {outfile}")
-    os.remove(tmp_aln)
+    run_cmd(f'rm {tmp_aln} {tmp_aln}.fai')
+
     return outfile