kkonganti@11: process {
kkonganti@11:     withName: 'SEQKIT_SEQ' {
kkonganti@11:         ext.args = [
kkonganti@11:             params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@11:         ].join(' ').trim()
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.dpubmlstpy_run) {
kkonganti@11:         withName: 'DOWNLOAD_PUBMLST_SCHEME' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.fastp_run) {
kkonganti@11:         withName: 'FASTP' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.mashscreen_run) {
kkonganti@11:         withName: 'MASH_SCREEN' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.tuspy_run) {
kkonganti@11:         withName: 'TOP_UNIQUE_SEROVARS' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.spades_run) {
kkonganti@11:         withName: 'SPADES_ASSEMBLE' {
kkonganti@11:             errorStrategy = 'ignore'
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.shovill_run) {
kkonganti@11:         withName: 'SHOVILL' {
kkonganti@11:             errorStrategy = 'ignore'
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}shovill.nf").shovillHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.polypolish_run) {
kkonganti@11:         withName: 'POLYPOLISH' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}polypolish.nf").polypolishHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.quast_run) {
kkonganti@11:         withName: 'QUAST' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}quast.nf").quastHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.pirate_run) {
kkonganti@11:         withName: 'PIRATE' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}pirate.nf").pirateHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.prodka_run) {
kkonganti@11:         withName: 'PRODIGAL' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}prodigal.nf").prodigalHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         withName: 'PROKKA' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}prokka.nf").prokkaHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.mlst_run) {
kkonganti@11:         withName: 'MLST' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.abricate_run) {
kkonganti@11:         withName: 'ABRICATE_RUN' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.mashtree_run) {
kkonganti@11:         withName: 'MASHTREE' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}mashtree.nf").mashtreeHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.upload_microreact) {
kkonganti@11:         withName: 'UPLOAD_MICROREACT' {
kkonganti@11:             errorStrategy = 'ignore'
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to instantiate a new function parser
kkonganti@11: // Need to refactor using ScriptParser... another day
kkonganti@11: def loadThisFunction (func_file) {
kkonganti@11:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@11:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@11:     return func
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to add relevant final parameters to summary log
kkonganti@11: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@11: 
kkonganti@11:     if (!params_to_add.isEmpty()) {
kkonganti@11:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@11:             it.value.clivalue != null && 
kkonganti@11:                 it.value.clivalue != '[:]' &&
kkonganti@11:                 it.value.clivalue != ''
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@11: 
kkonganti@11:         return not_null_params_to_add.collect {
kkonganti@11:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@11:         }.join(' ').trim()
kkonganti@11:     }
kkonganti@11:     return 1
kkonganti@11: }