diff --git a/modules/controlfreec/freec/main.nf b/modules/controlfreec/freec/main.nf index ba48ea1e..eb66eeaa 100644 --- a/modules/controlfreec/freec/main.nf +++ b/modules/controlfreec/freec/main.nf @@ -41,7 +41,7 @@ process CONTROLFREEC_FREEC { def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : "" def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : "" def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : "" - def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : "" + def coefficientofvariation = task.ext.args?["general"]?["coefficientofvariation"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : "" def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : "" def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : "" def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : ""