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task alignment_metrics: more resilient to large amplicon designs #435

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merged 3 commits into from
Sep 14, 2022
Merged

task alignment_metrics: more resilient to large amplicon designs #435

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a426368
expose parameters to samtools ampliconstats
dpark01 Jul 12, 2022
8c2e0a6
bump up default max amplicon length and count for samtools ampliconst…
dpark01 Sep 13, 2022
4b3605f
Merge branch 'master' into dp-stats
dpark01 Sep 13, 2022
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8 changes: 8 additions & 0 deletions pipes/WDL/tasks/tasks_reports.wdl
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Original file line number Diff line number Diff line change
@@ -1,12 +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=5000
Int? max_amplicons=500

Int? machine_mem_gb
String docker = "quay.io/broadinstitute/viral-core:2.1.33"
Expand Down Expand Up @@ -62,6 +68,8 @@ 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
Expand Down