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Increase Maximum Cycle Value for Base Recalibrator #459

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Increase Maximum Cycle Value for Base Recalibrator #459

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da7737c
modify maximum_cycle_value parameter
shadizaheri Jul 26, 2024
ec352ec
modify maximum_cycle_value parameter
shadizaheri Jul 26, 2024
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4 changes: 3 additions & 1 deletion wdl/pipelines/ILMN/Alignment/SRFlowcell.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
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5 changes: 4 additions & 1 deletion wdl/tasks/Utility/SRUtils.wdl
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Expand Up @@ -399,6 +399,7 @@ task BaseRecalibrator {
File known_sites_index

String prefix
Int maximum_cycle_value = 1000

RuntimeAttr? runtime_attr_override
}
Expand All @@ -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}


}
#########################
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