From a451199043cc59e2bf6cef5fac15b2ab32190c09 Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Wed, 24 Apr 2024 16:14:50 -0400 Subject: [PATCH] In align_and_count, change default to count only properly-paired reads Change the input, `filter_bam_to_proper_primary_mapped_reads`, in `align_and_count` to a default value of `true`; this changes the behavior of the task. Before filtering was available as an optional operation in `align_and_count`, reads were not filtered to proper pairs and later on the value of `filter_bam_to_proper_primary_mapped_reads=false` maintained the no-filter approach. With this commit, only properly-paired mapped reads are counted in `align_and_count`. --- pipes/WDL/tasks/tasks_reports.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/tasks/tasks_reports.wdl b/pipes/WDL/tasks/tasks_reports.wdl index 447580253..b30782838 100644 --- a/pipes/WDL/tasks/tasks_reports.wdl +++ b/pipes/WDL/tasks/tasks_reports.wdl @@ -392,7 +392,7 @@ task align_and_count { File ref_db Int topNHits = 3 - Boolean filter_bam_to_proper_primary_mapped_reads = false + Boolean filter_bam_to_proper_primary_mapped_reads = true Boolean do_not_require_proper_mapped_pairs_when_filtering = false Boolean keep_singletons_when_filtering = false Boolean keep_duplicates_when_filtering = false