From fc33686d93ae42a195ea21ce9fab9e0a5fb51cd3 Mon Sep 17 00:00:00 2001 From: Rhyker Ranallo-Benavidez Date: Fri, 27 Mar 2026 10:35:35 -0700 Subject: [PATCH] fix: guard against bioawk phantom empty record in fire_coverage/coverage division --- workflow/rules/fire-peaks.smk | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/workflow/rules/fire-peaks.smk b/workflow/rules/fire-peaks.smk index 07d15e0f6..f328534ab 100644 --- a/workflow/rules/fire-peaks.smk +++ b/workflow/rules/fire-peaks.smk @@ -198,7 +198,7 @@ rule helper_fdr_peaks_by_fire_elements: | bioawk -tc hdr '(NR==1)||($is_local_max=="true")' \ | csvtk filter -tT -C '$' -f "FDR<={params.max_peak_fdr}" \ | csvtk filter -tT -C '$' -f "fire_coverage>1" \ - | bioawk -tc hdr '(NR==1)||($fire_coverage/$coverage>={params.min_per_acc_peak})' \ + | bioawk -tc hdr '(NR==1)||(NF>0 && $fire_coverage/$coverage>={params.min_per_acc_peak})' \ | bedtools intersect -wa -wb -sorted -a - \ -b <(tabix {input.fire} {wildcards.chrom} \ | cut -f 1-3 \ @@ -295,8 +295,7 @@ rule wide_fire_peaks: ( \ bgzip -cd {input.bed}; \ bioawk -tc hdr 'NR==1 || $FDR<={params.max_peak_fdr}' {input.track} \ - | bioawk -tc hdr 'NR==1 || $coverage>0' \ - | bioawk -tc hdr 'NR==1 || ($fire_coverage/$coverage>={params.min_frac_acc})' \ + | bioawk -tc hdr 'NR==1 || (NF>0 && $coverage>0 && $fire_coverage/$coverage>={params.min_frac_acc})' \ ) \ | cut -f 1-3 \ | bedtools sort \