kkonganti@0: process {
kkonganti@0:     withName: 'SEQKIT_SEQ' {
kkonganti@0:         ext.args = [
kkonganti@0:             params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
kkonganti@0:         ].join(' ').trim()
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     // withName: 'SAMTOOLS_FASTQ' {
kkonganti@0:     //     ext.args = (params.fq_single_end ? '-F 4' : '-f 2')
kkonganti@0:     // }
kkonganti@0: 
kkonganti@0:     if (params.fastp_run) {
kkonganti@0:         withName: 'FASTP' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.kmaalign_run) {
kkonganti@0:         withName: 'KMA_ALIGN' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.seqkit_grep_run) {
kkonganti@0:         withName: 'SEQKIT_GREP' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.salmonidx_run){
kkonganti@0:         withName: 'SALMON_INDEX' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0: 
kkonganti@0:         withName: 'SALMON_QUANT' {
kkonganti@0:             errorStrategy = 'ignore'
kkonganti@0:             ext.args = '--minAssignedFrags 1'
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.sourmashsketch_run) {
kkonganti@0:         withName: 'SOURMASH_SKETCH' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.sourmashgather_run) {
kkonganti@0:         withName: 'SOURMASH_GATHER' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
kkonganti@0:             )
kkonganti@0: 
kkonganti@0:             if (params.sfhpy_run) {
kkonganti@0:                 ext.args2 = addParamsToSummary(
kkonganti@0:                     loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
kkonganti@0:                 )
kkonganti@0:             }
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     // if (params.sourmashtaxmetagenome_run) {
kkonganti@0:     //     withName: 'SOURMASH_TAX_METAGENOME' {
kkonganti@0:     //         ext.args = addParamsToSummary(
kkonganti@0:     //             loadThisFunction("${params.toolshelp}${params.fs}sourmashtaxmetagenome.nf").sourmashtaxmetagenomeHelp(params).helpparams
kkonganti@0:     //         )
kkonganti@0:     //     }
kkonganti@0:     // }
kkonganti@0: 
kkonganti@0:     if (params.gsalkronapy_run) {
kkonganti@0:         withName: 'NOWAYOUT_RESULTS' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}gsalkronapy.nf").gsalkronapyHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: 
kkonganti@0:     if (params.krona_ktIT_run) {
kkonganti@0:         withName: 'KRONA_KTIMPORTTEXT' {
kkonganti@0:             ext.args = addParamsToSummary(
kkonganti@0:                 loadThisFunction("${params.toolshelp}${params.fs}kronaktimporttext.nf").kronaktimporttextHelp(params).helpparams
kkonganti@0:             )
kkonganti@0:         }
kkonganti@0:     }
kkonganti@0: }
kkonganti@0: 
kkonganti@0: // Method to instantiate a new function parser
kkonganti@0: // Need to refactor using ScriptParser... another day
kkonganti@0: def loadThisFunction (func_file) {
kkonganti@0:     GroovyShell grvy_sh = new GroovyShell()
kkonganti@0:     def func = grvy_sh.parse(new File ( func_file ) )
kkonganti@0:     return func
kkonganti@0: }
kkonganti@0: 
kkonganti@0: // Method to add relevant final parameters to summary log
kkonganti@0: def addParamsToSummary(Map params_to_add = [:]) {
kkonganti@0: 
kkonganti@0:     if (!params_to_add.isEmpty()) {
kkonganti@0:         def not_null_params_to_add = params_to_add.findAll {
kkonganti@0:             it.value.clivalue != null && 
kkonganti@0:                 it.value.clivalue != '[:]' &&
kkonganti@0:                 it.value.clivalue != ''
kkonganti@0:         }
kkonganti@0: 
kkonganti@0:         params.logtheseparams += not_null_params_to_add.keySet().toList()
kkonganti@0: 
kkonganti@0:         return not_null_params_to_add.collect {
kkonganti@0:             "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
kkonganti@0:         }.join(' ').trim()
kkonganti@0:     }
kkonganti@0:     return 1
kkonganti@0: }