kkonganti@1: process {
kkonganti@1:     withName: 'DB_PER_COMPUTED_SEROTYPE' {
kkonganti@1:         ext.args = addParamsToSummary(
kkonganti@1:             loadThisFunction("${params.toolshelp}${params.fs}wcomp.nf").wcompHelp(params).helpparams
kkonganti@1:         )
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     withName: 'DB_PER_SNP_CLUSTER' {
kkonganti@1:         ext.args = addParamsToSummary(
kkonganti@1:             loadThisFunction("${params.toolshelp}${params.fs}wsnp.nf").wsnpHelp(params).helpparams
kkonganti@1:         )
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     if (params.mashsketch_run) {
kkonganti@1:         withName: 'MASH_SKETCH' {
kkonganti@1:             ext.args = addParamsToSummary(
kkonganti@1:                 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
kkonganti@1:             )
kkonganti@1:         }
kkonganti@1:     }
kkonganti@1: 
kkonganti@1:     withName: 'SCAFFOLD_GENOMES' {
kkonganti@1:         maxRetries = 5
kkonganti@1:         publishDir = [
kkonganti@1:             path:  "${params.output}${params.fs}scaffold_genomes",
kkonganti@1:             mode: "move",
kkonganti@1:             overwrite: true,
kkonganti@1:             saveAs: { filename -> filename ==~ /versions\.yml|genome_paths\.txt/ ? null : filename }
kkonganti@1:         ]
kkonganti@1:     }
kkonganti@1: }
kkonganti@1: 
kkonganti@1: 
kkonganti@1: // Parse the default params
kkonganti@1: def loadThisFunction (func_file) {
kkonganti@1:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@1:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@1:     return func
kkonganti@1: }
kkonganti@1: 
kkonganti@1: // Method to add relevant final parameters to summary log
kkonganti@1: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@1: 
kkonganti@1:     if (!params_to_add.isEmpty()) {
kkonganti@1:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@1:             it.value.clivalue != null && 
kkonganti@1:                 it.value.clivalue != '[:]' &&
kkonganti@1:                 it.value.clivalue != ''
kkonganti@1:         }
kkonganti@1: 
kkonganti@1:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@1: 
kkonganti@1:         return not_null_params_to_add.collect {
kkonganti@1:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@1:         }.join(' ').trim()
kkonganti@1:     }
kkonganti@1:     return 1
kkonganti@1: }