From da7737cf25d8a71d81e2e8d7a5762e1181132aa8 Mon Sep 17 00:00:00 2001 From: Shadi Zaheri Date: Fri, 26 Jul 2024 08:08:57 -0400 Subject: [PATCH 1/2] modify maximum_cycle_value parameter --- wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl b/wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl index 6af33fe47..bdb0e7898 100644 --- a/wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl +++ b/wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl @@ -191,7 +191,9 @@ workflow SRFlowcell { known_sites_vcf = ref_map["known_sites_vcf"], known_sites_index = ref_map["known_sites_index"], - prefix = SM + ".baseRecalibratorReport" + prefix = SM + ".baseRecalibratorReport", + maximum_cycle_value = 1000 + } call SRUTIL.ApplyBQSR as t_010_ApplyBQSR { From ec352ec83dade56c77b1f5ced9eb921d977a1b30 Mon Sep 17 00:00:00 2001 From: Shadi Zaheri Date: Fri, 26 Jul 2024 08:09:48 -0400 Subject: [PATCH 2/2] modify maximum_cycle_value parameter --- wdl/tasks/Utility/SRUtils.wdl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wdl/tasks/Utility/SRUtils.wdl b/wdl/tasks/Utility/SRUtils.wdl index 869b9dc92..fd08624c1 100644 --- a/wdl/tasks/Utility/SRUtils.wdl +++ b/wdl/tasks/Utility/SRUtils.wdl @@ -399,6 +399,7 @@ task BaseRecalibrator { File known_sites_index String prefix + Int maximum_cycle_value = 1000 RuntimeAttr? runtime_attr_override } @@ -425,7 +426,9 @@ task BaseRecalibrator { -I ~{input_bam} \ --use-original-qualities \ -O ~{prefix}.txt \ - --known-sites ~{known_sites_vcf} + --known-sites ~{known_sites_vcf} \ + --maximum-cycle-value ~{maximum_cycle_value} + } #########################