kkonganti@0: process {
kkonganti@0:     if (params.dpubmlstpy_run) {
kkonganti@0:         withName: 'DOWNLOAD_PUBMLST_SCHEME' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.checkm2predict_run) {
kkonganti@0:         withName: 'CHECKM2_PREDICT' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}checkm2predict.nf").checkm2predictHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.guncrun_run) {
kkonganti@0:         withName: 'GUNC_RUN' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}guncrun.nf").guncrunHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.mlst_run) {
kkonganti@0:         withName: 'MLST' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.mashsketch_run) {
kkonganti@0:         withName: 'MASH_SKETCH' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: // Method to instantiate a new function parser
kkonganti@0: // Need to refactor using ScriptParser... another day
kkonganti@0: def loadThisFunction (func_file) {
kkonganti@0:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@0:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@0:     return func
kkonganti@0: }
kkonganti@0: 
kkonganti@0: // Method to add relevant final parameters to summary log
kkonganti@0: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@0: 
kkonganti@0:     if (!params_to_add.isEmpty()) {
kkonganti@0:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@0:             it.value.clivalue != null && 
kkonganti@0:                 it.value.clivalue != '[:]' &&
kkonganti@0:                 it.value.clivalue != ''
kkonganti@0:         }
kkonganti@0: 
kkonganti@0:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@0: 
kkonganti@0:         return not_null_params_to_add.collect {
kkonganti@0:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@0:         }.join(' ').trim()
kkonganti@0:     }
kkonganti@0:     return 1
kkonganti@0: }