From 33ab0268ed6126d5c63e56632d22c2e508ebe4dd Mon Sep 17 00:00:00 2001 From: fraser-combe Date: Thu, 3 Oct 2024 10:44:09 -0500 Subject: [PATCH] combine flu and non flu into same mapped reads output --- workflows/theiacov/wf_theiacov_ont.wdl | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/workflows/theiacov/wf_theiacov_ont.wdl b/workflows/theiacov/wf_theiacov_ont.wdl index 7c34a744b..3cda26887 100644 --- a/workflows/theiacov/wf_theiacov_ont.wdl +++ b/workflows/theiacov/wf_theiacov_ont.wdl @@ -434,10 +434,6 @@ workflow theiacov_ont { File? qc_standard = qc_check_task.qc_standard # Non-flu specific outputs # Non-flu specific outputs - Float percentage_mapped_reads = select_first([stats_n_coverage.percentage_mapped_reads, 0.0]) - Float percentage_mapped_reads_trimmed = select_first([stats_n_coverage_primtrim.percentage_mapped_reads, 0.0]) - - # Flu-specific outputs - Float percentage_mapped_reads_flu = select_first([flu_stats_n_coverage.percentage_mapped_reads, 0.0]) + Float percentage_mapped_reads = select_first([flu_stats_n_coverage.percentage_mapped_reads, stats_n_coverage.percentage_mapped_reads, 0.0]) } } \ No newline at end of file