authorized several steps into --step

main.nf

@@ -87,12 +87,14 @@
   */
 
 // Show help message.
+
 if (params.help){
   helpMessage()
   exit 0
 }
 
-// Define list of available steps
+// Define list of available steps.
+
 def defineStepList() {
     return [
         '01_clean_qc',
@@ -106,7 +108,7 @@ def defineStepList() {
     ]
 }
 
-// Check step existence
+// Check step existence.
 
 def checkParameterExistence(list_it, list) {
     nb_false_step = 0
@@ -120,27 +122,13 @@ def checkParameterExistence(list_it, list) {
     else {return true}
 }
 
-// Check number of steps
-def numberParameter(list_it, list) {
-    nb_step = 0
-    filtering_step = false
-    for(it in list_it) {
-        nb_step = nb_step + 1
-        if(it == '03_filtering') {filtering_step = true}
-    }
-    if(nb_step > 2) {return false}
-    else {
-        if((nb_step == 2) && (!filtering_step)){return false}
-        else {return true}
-    }
-}
+// Check number of steps.
 
 // Set up parameters.
 
 step = params.step.split(",")
 stepList = defineStepList()
-if (!checkParameterExistence(step, stepList)) exit 1, "Unknown step ${step}, see --help for more information"
-if (!numberParameter(step, stepList)) exit 1, "You can choose one step (or two step only if one of two is 03_filtering step)"
+if (!checkParameterExistence(step, stepList)) exit 1, "Unknown step(s) upon ${step}, see --help for more information"
 
 if (!['metaspades','megahit'].contains(params.assembly)){
     exit 1, "Invalid aligner option: ${params.assembly}. Valid options: 'metaspades', 'megahit'"