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In align_and_count, change default to count only properly-paired reads #534

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In align_and_count, change default to count only properly-paired reads #534

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In align_and_count, change default to count only properly-paired reads
tomkinsc Apr 24, 2024
4f074b4
Merge branch 'master' into ct-align_and_count-filter-to-proper-by-def…
tomkinsc Jun 4, 2024
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2 changes: 1 addition & 1 deletion pipes/WDL/tasks/tasks_reports.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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