From 5bc13c7699bbde13d27559a245b4df3908050b8e Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 2 Oct 2024 14:45:57 -0500 Subject: [PATCH] Fix bugs --- definitions/tools/bam_readcount.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/definitions/tools/bam_readcount.wdl b/definitions/tools/bam_readcount.wdl index 3c3e4a71..4c8ae8e8 100644 --- a/definitions/tools/bam_readcount.wdl +++ b/definitions/tools/bam_readcount.wdl @@ -65,9 +65,9 @@ task bamReadcount { sample_index = vcf_file.samples.index(sample) snv_region_fh = tempfile.NamedTemporaryFile("w", delete=False) - snv_region_writer = csv.writer(fh, delimiter="\t") + snv_region_writer = csv.writer(snv_region_fh, delimiter="\t") indel_region_fh = tempfile.NamedTemporaryFile("w", delete=False) - indel_region_writer = csv.writer(fh, delimiter="\t") + indel_region_writer = csv.writer(indel_region_fh, delimiter="\t") for variant in vcf_file: ref = variant.REF chr = variant.CHROM