--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/workflows/conf/process/centriflaken_hy.process.config	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,129 @@
+process {
+    withName: 'SEQKIT_SEQ' {
+        ext.args = [
+            params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
+        ].join(' ').trim()
+    }
+
+    if (params.seqkit_rmdup_run) {
+        withName: 'SEQKIT_RMDUP' {
+            ext.when = params.seqkit_rmdup_run
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.seqkit_grep_on) {
+        withName: 'SEQKIT_GREP' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
+            )
+        }
+    }
+
+    withName: 'CENTRIFUGE_CLASSIFY' {
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
+        )
+    }
+
+    withName: 'KRAKEN2_CLASSIFY' {
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
+        )
+    }
+
+    withName: 'MEGAHIT_ASSEMBLE' {
+        ext.when = params.megahit_run
+        errorStrategy = 'ignore'
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
+        )
+    }
+
+    withName: 'SPADES_ASSEMBLE' {
+        ext.when = params.spades_run
+        errorStrategy = 'ignore'
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
+        )
+    }
+
+    if (params.ectyper_run) {
+        withName: 'ECTYPER' {
+            ext.when = params.ectyper_run
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
+            )
+        }
+    }
+
+    withName: 'SEROTYPEFINDER' {
+        ext.when = params.serotypefinder_run
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
+        )
+    }
+
+    withName: 'SEQSERO2' {
+        ext.when = params.seqsero2_run
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
+        )
+    }
+
+    withName: 'MLST' {
+        ext.when = params.mlst_run
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
+        )
+    }
+
+    if (params.amrfinderplus_run) {    
+        withName: 'AMRFINDERPLUS_RUN' {
+            ext.when = params.amrfinderplus_run
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
+            )
+        }
+    }
+
+    withName: 'ABRICATE_RUN' {
+        ext.when = params.abricate_run
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
+        )
+    }
+
+    withName: 'ABRICATE_SUMMARY' {
+        ext.when = params.abricate_summary_run
+    }
+}
+
+// Method to instantiate a new function parser
+// Need to refactor using ScriptParser... another day
+def loadThisFunction (func_file) {
+    GroovyShell grvy_sh = new GroovyShell()
+    def func = grvy_sh.parse(new File ( func_file ) )
+    return func
+}
+
+// Method to add relevant final parameters to summary log
+def addParamsToSummary(Map params_to_add = [:]) {
+
+    if (!params_to_add.isEmpty()) {
+        def not_null_params_to_add = params_to_add.findAll {
+            it.value.clivalue != null && 
+                it.value.clivalue != '[:]' &&
+                it.value.clivalue != ''
+        }
+
+        params.logtheseparams += not_null_params_to_add.keySet().toList()
+
+        return not_null_params_to_add.collect {
+            "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
+        }.join(' ').trim()
+    }
+    return 1
+}
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