From 5bcaff70d17364d95fbd43e5c8f0e9f83e868ec6 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Mon, 23 Sep 2024 09:22:01 +0100 Subject: [PATCH] adjust output filename --- README.md | 2 +- src/vcf_qc.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 59abda7..bb8dd27 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ This app should be executed stand-alone or as part of a DNAnexus workflow for a The app requires a VCF file (.vcf) containing variants to be evaluated and a bed file defining the regions within which variants in the vcf should be evaluated. ## What does this app output? -The app outputs one tab delimited file `[vcf_prefix].vcf.qc`, where `vcf_prefix` is the vcf filename without extension: +The app outputs one tab delimited file `[vcf_prefix].vcf.QC`, where `vcf_prefix` is the vcf filename without extension: * sample id * mean het ratio (mean AAF of het variants) diff --git a/src/vcf_qc.py b/src/vcf_qc.py index d63b52b..c94f009 100644 --- a/src/vcf_qc.py +++ b/src/vcf_qc.py @@ -300,7 +300,7 @@ def main(vcf_file, bed_file): het_hom_counts = get_het_hom_counts(vcf=tmp_vcf) ratios = calculate_ratios(counts=het_hom_counts) - outfile = f"{re.sub(r'.vcf(.gz)?$', '', vcf_file)}.vcf.qc" + outfile = f"{re.sub(r'.vcf(.gz)?$', '', vcf_file)}.vcf.QC" if os.path.exists("/home/dnanexus"): write_output_file(outfile=outfile, ratios=ratios)