--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.6.1/workflows/conf/process/bettercallsal.process.config	Tue Sep 05 11:51:40 2023 -0400
@@ -0,0 +1,173 @@
+process {
+    withName: 'SEQKIT_SEQ' {
+        ext.args = [
+            params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
+        ].join(' ').trim()
+    }
+
+    if (params.bbmerge_run) {
+        withName: 'BBTOOLS_BBMERGE' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.fastp_run) {
+        withName: 'FASTP' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.bcs_concat_pe) {
+        withName: 'CAT_CAT' {
+            ext.prefix = 'concat.fastq.gz'
+        }
+    }
+
+
+    if (params.mashscreen_run) {
+        withName: 'MASH_SCREEN' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.tuspy_run) {
+        withName: 'TOP_UNIQUE_SEROVARS' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.gsrpy_run) {
+        withName: 'BCS_RESULTS' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.sourmashsketch_run) {
+        withName: 'SOURMASH_SKETCH' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${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}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
+                )
+            }
+        }
+    }
+
+    if (params.sourmashsearch_run) {
+        withName: 'SOURMASH_SEARCH' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
+            )
+
+            if (params.sfhpy_run) {
+                ext.args2 = addParamsToSummary(
+                    loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
+                )
+            }
+        }
+    }
+
+    if (params.kmaindex_run) {
+        withName: 'KMA_INDEX' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.kmaalign_run) {
+        withName: 'KMA_ALIGN' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
+            )
+        }
+    }
+
+    if (params.megahit_run) {
+        withName: 'MEGAHIT_ASSEMBLE' {
+            errorStrategy = 'ignore'
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
+            )
+        }
+
+        withName: 'MLST' {
+            ext.when = params.mlst_run
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
+            )
+        }
+
+        withName: 'ABRICATE_RUN' {
+            ext.when = params.abricate_run
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
+            )
+        }
+
+        withName: 'ABRICATE_SUMMARY' {
+            ext.when = params.abricate_summary_run
+        }
+    }
+
+    if (params.salmonidx_run){
+        withName: 'SALMON_INDEX' {
+            ext.args = addParamsToSummary(
+                loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
+            )
+        }
+    }
+
+    withName: 'OTF_GENOME' {
+        errorStrategy = 'ignore'
+    }
+    
+}
+
+
+// Parse the default params
+def loadThisFunction (func_file) {
+    GroovyShell grvy_sh = new GroovyShell()
+    def func = grvy_sh.parse(new File ( func_file ) )
+    return func
+}
+
+// Method to add relevant final parameters to summary log
+def addParamsToSummary(Map params_to_add = [:]) {
+
+    if (!params_to_add.isEmpty()) {
+        def not_null_params_to_add = params_to_add.findAll {
+            it.value.clivalue != null && 
+                it.value.clivalue != '[:]' &&
+                it.value.clivalue != ''
+        }
+
+        params.logtheseparams += not_null_params_to_add.keySet().toList()
+
+        return not_null_params_to_add.collect {
+            "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
+        }.join(' ').trim()
+    }
+    return 1
+}