kkonganti@11: process {
kkonganti@11:     withName: 'SEQKIT_SEQ' {
kkonganti@11:         ext.args = [
kkonganti@11:             params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@11:         ].join(' ').trim()
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.bbmerge_run) {
kkonganti@11:         withName: 'BBTOOLS_BBMERGE' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.fastp_run) {
kkonganti@11:         withName: 'FASTP' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.bcs_concat_pe) {
kkonganti@11:         withName: 'CAT_CAT' {
kkonganti@11:             ext.prefix = 'concat.fastq.gz'
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11: 
kkonganti@11:     if (params.mashscreen_run) {
kkonganti@11:         withName: 'MASH_SCREEN' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${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}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.gsrpy_run) {
kkonganti@11:         withName: 'BCS_RESULTS' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.sourmashsketch_run) {
kkonganti@11:         withName: 'SOURMASH_SKETCH' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.sourmashgather_run) {
kkonganti@11:         withName: 'SOURMASH_GATHER' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             if (params.sfhpy_run) {
kkonganti@11:                 ext.args2 = addParamsToSummary(
kkonganti@11:                     loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@11:                 )
kkonganti@11:             }
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.sourmashsearch_run) {
kkonganti@11:         withName: 'SOURMASH_SEARCH' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
kkonganti@11:             )
kkonganti@11: 
kkonganti@11:             if (params.sfhpy_run) {
kkonganti@11:                 ext.args2 = addParamsToSummary(
kkonganti@11:                     loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@11:                 )
kkonganti@11:             }
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.kmaindex_run) {
kkonganti@11:         withName: 'KMA_INDEX' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.kmaalign_run) {
kkonganti@11:         withName: 'KMA_ALIGN' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.megahit_run) {
kkonganti@11:         withName: 'MEGAHIT_ASSEMBLE' {
kkonganti@11:             errorStrategy = 'ignore'
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         withName: 'MLST' {
kkonganti@11:             ext.when = params.mlst_run
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         withName: 'ABRICATE_RUN' {
kkonganti@11:             ext.when = params.abricate_run
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         withName: 'ABRICATE_SUMMARY' {
kkonganti@11:             ext.when = params.abricate_summary_run
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (params.salmonidx_run){
kkonganti@11:         withName: 'SALMON_INDEX' {
kkonganti@11:             ext.args = addParamsToSummary(
kkonganti@11:                 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
kkonganti@11:             )
kkonganti@11:         }
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     withName: 'OTF_GENOME' {
kkonganti@11:         errorStrategy = 'ignore'
kkonganti@11:     }
kkonganti@11:     
kkonganti@11: }
kkonganti@11: 
kkonganti@11: 
kkonganti@11: // Parse the default params
kkonganti@11: def loadThisFunction (func_file) {
kkonganti@11:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@11:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@11:     return func
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to add relevant final parameters to summary log
kkonganti@11: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@11: 
kkonganti@11:     if (!params_to_add.isEmpty()) {
kkonganti@11:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@11:             it.value.clivalue != null && 
kkonganti@11:                 it.value.clivalue != '[:]' &&
kkonganti@11:                 it.value.clivalue != ''
kkonganti@11:         }
kkonganti@11: 
kkonganti@11:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@11: 
kkonganti@11:         return not_null_params_to_add.collect {
kkonganti@11:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@11:         }.join(' ').trim()
kkonganti@11:     }
kkonganti@11:     return 1
kkonganti@11: }