From 0467dcf8765dd2e564a8d4bc103c863e2a5ad846 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Fri, 10 Feb 2023 09:06:25 -0500 Subject: [PATCH] samtools ampliconstats needs bed in certain order --- pipes/WDL/tasks/tasks_reports.wdl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index b695ea7ea..41c56cb3c 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -67,11 +67,12 @@ task alignment_metrics { echo -e "sample_sanitized\tbam\tamplicon_set\tamplicon_idx\tamplicon_left\tamplicon_right\tFREADS\tFDEPTH\tFPCOV\tFAMP" > "~{out_basename}.ampliconstats_parsed.txt" if [ -n "~{primers_bed}" ]; then # samtools ampliconstats + cat "~{primers_bed}" | sort -k 4 -t $'\t' > primers-sorted_for_samtools.bed samtools ampliconstats -s -@ $(nproc) \ ~{'-d ' + min_coverage} \ ~{'-l ' + max_amp_len} \ ~{'-a ' + max_amplicons} \ - -o "~{out_basename}".ampliconstats.txt "~{primers_bed}" "~{aligned_bam}" + -o "~{out_basename}".ampliconstats.txt primers-sorted_for_samtools.bed "~{aligned_bam}" # parse into our own tsv to facilitate tsv joining later if [ -n "~{default='' amplicon_set}" ]; then