--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/workflows/conf/process/bettercallsal_db.process.config	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,58 @@
+process {
+    withName: 'DB_PER_COMPUTED_SEROTYPE' {
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}wcomp.nf").wcompHelp(params).helpparams
+        )
+    }
+
+    withName: 'DB_PER_SNP_CLUSTER' {
+        ext.args = addParamsToSummary(
+            loadThisFunction("${params.toolshelp}${params.fs}wsnp.nf").wsnpHelp(params).helpparams
+        )
+    }
+
+    if (params.mashsketch_run) {
+        withName: 'MASH_SKETCH' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
+            )
+        }
+    }
+
+    withName: 'SCAFFOLD_GENOMES' {
+        maxRetries = 5
+        publishDir = [
+            path:  "${params.output}${params.fs}scaffold_genomes",
+            mode: "move",
+            overwrite: true,
+            saveAs: { filename -> filename ==~ /versions\.yml|genome_paths\.txt/ ? null : filename }
+        ]
+    }
+}
+
+
+// Parse the default params
+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
+}