From a426368b31adb5b79102c6f99077e29681085778 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 12 Jul 2022 07:31:07 -0400 Subject: [PATCH 1/2] expose parameters to samtools ampliconstats --- pipes/WDL/tasks/tasks_reports.wdl | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index 43ee24a90..9ab084a7b 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -7,6 +7,8 @@ task alignment_metrics { File? primers_bed String? amplicon_set Int? min_coverage + Int? max_amp_len + Int? max_amplicons Int? machine_mem_gb String docker = "quay.io/broadinstitute/viral-core:2.1.33" @@ -62,6 +64,8 @@ task alignment_metrics { # samtools ampliconstats samtools ampliconstats -s -@ $(nproc) \ ~{'-d ' + min_coverage} \ + ~{'-l ' + max_amp_len} \ + ~{'-a ' + max_amplicons} \ -o "~{out_basename}".ampliconstats.txt "~{primers_bed}" "~{aligned_bam}" # parse into our own tsv to facilitate tsv joining later From 8c2e0a622eb0701ee51070580b3b283c49efdd7f Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 13 Sep 2022 17:56:26 -0400 Subject: [PATCH 2/2] bump up default max amplicon length and count for samtools ampliconstats (no reason not to) --- pipes/WDL/tasks/tasks_reports.wdl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index 9ab084a7b..9de1b41b7 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -1,14 +1,18 @@ version 1.0 task alignment_metrics { + meta { + description: "Produce various standard metrics and coverage plots via Picard and Samtools for aligned BAM files." + } + input { File aligned_bam File ref_fasta File? primers_bed String? amplicon_set Int? min_coverage - Int? max_amp_len - Int? max_amplicons + Int? max_amp_len=5000 + Int? max_amplicons=500 Int? machine_mem_gb String docker = "quay.io/broadinstitute/viral-core:2.1.33"