--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/workflows/conf/process/nowayout.process.config	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,121 @@
+process {
+    withName: 'SEQKIT_SEQ' {
+        ext.args = [
+            params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
+        ].join(' ').trim()
+    }
+
+    // withName: 'SAMTOOLS_FASTQ' {
+    //     ext.args = (params.fq_single_end ? '-F 4' : '-f 2')
+    // }
+
+    if (params.fastp_run) {
+        withName: 'FASTP' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.kmaalign_run) {
+        withName: 'KMA_ALIGN' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.seqkit_grep_run) {
+        withName: 'SEQKIT_GREP' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.salmonidx_run){
+        withName: 'SALMON_INDEX' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
+            )
+        }
+
+        withName: 'SALMON_QUANT' {
+            errorStrategy = 'ignore'
+            ext.args = '--minAssignedFrags 1'
+        }
+    }
+
+    if (params.sourmashsketch_run) {
+        withName: 'SOURMASH_SKETCH' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.sourmashgather_run) {
+        withName: 'SOURMASH_GATHER' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
+            )
+
+            if (params.sfhpy_run) {
+                ext.args2 = addParamsToSummary(
+                    loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
+                )
+            }
+        }
+    }
+
+    // if (params.sourmashtaxmetagenome_run) {
+    //     withName: 'SOURMASH_TAX_METAGENOME' {
+    //         ext.args = addParamsToSummary(
+    //             loadThisFunction("${params.toolshelp}${params.fs}sourmashtaxmetagenome.nf").sourmashtaxmetagenomeHelp(params).helpparams
+    //         )
+    //     }
+    // }
+
+    if (params.gsalkronapy_run) {
+        withName: 'NOWAYOUT_RESULTS' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}gsalkronapy.nf").gsalkronapyHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.krona_ktIT_run) {
+        withName: 'KRONA_KTIMPORTTEXT' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}kronaktimporttext.nf").kronaktimporttextHelp(params).helpparams
+            )
+        }
+    }
+}
+
+// Method to instantiate a new function parser
+// Need to refactor using ScriptParser... another day
+def loadThisFunction (func_file) {
+    GroovyShell grvy_sh = new GroovyShell()
+    def func = grvy_sh.parse(new File ( func_file ) )
+    return func
+}
+
+// Method to add relevant final parameters to summary log
+def addParamsToSummary(Map params_to_add = [:]) {
+
+    if (!params_to_add.isEmpty()) {
+        def not_null_params_to_add = params_to_add.findAll {
+            it.value.clivalue != null && 
+                it.value.clivalue != '[:]' &&
+                it.value.clivalue != ''
+        }
+
+        params.logtheseparams += not_null_params_to_add.keySet().toList()
+
+        return not_null_params_to_add.collect {
+            "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
+        }.join(' ').trim()
+    }
+    return 1
+}
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