Merge branch 'master' into pangolin

broadinstitute · Sep 14, 2022 · f2271ae · f2271ae
2 parents 31e53b3 + 39b4e77
commit f2271ae
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl
@@ -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"
@@ -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