diff --git a/bio/ngscheckmate/makesnvpattern/wrapper.py b/bio/ngscheckmate/makesnvpattern/wrapper.py index 0553fabb42..1045acd689 100644 --- a/bio/ngscheckmate/makesnvpattern/wrapper.py +++ b/bio/ngscheckmate/makesnvpattern/wrapper.py @@ -25,18 +25,18 @@ # Ensure user can name each file according to their need output_mapping = { - "bowtie": f"'{tempdir}/snake_out.bowtieout'", - "fasta": f"'{tempdir}/snake_out.fasta'", - "ntm": f"'{tempdir}/snake_out.ntm'", - "pattern": f"'{tempdir}/snake_out.pt'", - "pattern_text": f"'{tempdir}/snake_out.pt-txt'", - "pattern_sorted": f"'{tempdir}/snake_out.pt-txt.sorted'", - "text": f"'{tempdir}/snake_out.txt'", - "uniq": f"'{tempdir}/snake_out.uniq.txt'", - "txt_sorted": f"'{tempdir}/snake_out.uniq.txt.sorted'", + "bowtie": f"{tempdir}/snake_out.bowtieout", + "fasta": f"{tempdir}/snake_out.fasta", + "ntm": f"{tempdir}/snake_out.ntm", + "pattern": f"{tempdir}/snake_out.pt", + "pattern_text": f"{tempdir}/snake_out.pt-txt", + "pattern_sorted": f"{tempdir}/snake_out.pt-txt.sorted", + "text": f"{tempdir}/snake_out.txt", + "uniq": f"{tempdir}/snake_out.uniq.txt", + "txt_sorted": f"{tempdir}/snake_out.uniq.txt.sorted", } for output_key, temp_file in output_mapping.items(): output_path = snakemake.output.get(output_key) if output_path: - shell(f"mv --verbose {temp_file:q} {output_path:q} {log}") + shell("mv --verbose {temp_file:q} {output_path:q} {log}")