kkonganti@105: process {
kkonganti@105:     withName: 'SEQKIT_SEQ' {
kkonganti@105:         ext.args = [
kkonganti@105:             params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@105:         ].join(' ').trim()
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     if (params.seqkit_rmdup_run) {
kkonganti@105:         withName: 'SEQKIT_RMDUP' {
kkonganti@105:             ext.when = params.seqkit_rmdup_run
kkonganti@105:             ext.args = addParamsToSummary(
kkonganti@105:                 loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
kkonganti@105:             )
kkonganti@105:         }
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     if (params.seqkit_grep_on) {
kkonganti@105:         withName: 'SEQKIT_GREP' {
kkonganti@105:             ext.args = addParamsToSummary(
kkonganti@105:                 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
kkonganti@105:             )
kkonganti@105:         }
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'KRAKEN2_CLASSIFY' {
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@105:         ext.when = params.megahit_run
kkonganti@105:         errorStrategy = 'ignore'
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'SPADES_ASSEMBLE' {
kkonganti@105:         ext.when = params.spades_run
kkonganti@105:         errorStrategy = 'ignore'
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     if (params.ectyper_run) {
kkonganti@105:         withName: 'ECTYPER' {
kkonganti@105:             ext.when = params.ectyper_run
kkonganti@105:             ext.args = addParamsToSummary(
kkonganti@105:                 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
kkonganti@105:             )
kkonganti@105:         }
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'SEROTYPEFINDER' {
kkonganti@105:         ext.when = params.serotypefinder_run
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'SEQSERO2' {
kkonganti@105:         ext.when = params.seqsero2_run
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'MLST' {
kkonganti@105:         ext.when = params.mlst_run
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     if (params.amrfinderplus_run) {    
kkonganti@105:         withName: 'AMRFINDERPLUS_RUN' {
kkonganti@105:             ext.when = params.amrfinderplus_run
kkonganti@105:             ext.args = addParamsToSummary(
kkonganti@105:                 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
kkonganti@105:             )
kkonganti@105:         }
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'ABRICATE_RUN' {
kkonganti@105:         ext.when = params.abricate_run
kkonganti@105:         ext.args = addParamsToSummary(
kkonganti@105:             loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@105:         )
kkonganti@105:     }
kkonganti@105: 
kkonganti@105:     withName: 'ABRICATE_SUMMARY' {
kkonganti@105:         ext.when = params.abricate_summary_run
kkonganti@105:     }
kkonganti@105: }
kkonganti@105: 
kkonganti@105: // Method to instantiate a new function parser
kkonganti@105: // Need to refactor using ScriptParser... another day
kkonganti@105: def loadThisFunction (func_file) {
kkonganti@105:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@105:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@105:     return func
kkonganti@105: }
kkonganti@105: 
kkonganti@105: // Method to add relevant final parameters to summary log
kkonganti@105: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@105: 
kkonganti@105:     if (!params_to_add.isEmpty()) {
kkonganti@105:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@105:             it.value.clivalue != null && 
kkonganti@105:                 it.value.clivalue != '[:]' &&
kkonganti@105:                 it.value.clivalue != ''
kkonganti@105:         }
kkonganti@105: 
kkonganti@105:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@105: 
kkonganti@105:         return not_null_params_to_add.collect {
kkonganti@105:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@105:         }.join(' ').trim()
kkonganti@105:     }
kkonganti@105:     return 1
kkonganti@105: }