--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/nextflow.config	Fri May 29 13:27:47 2026 +0000
@@ -0,0 +1,38 @@
+def fs = File.separator
+def pd = "${projectDir}"
+
+// Global parameters
+includeConfig "${pd}${fs}conf${fs}manifest.config"
+includeConfig "${pd}${fs}conf${fs}base.config"
+
+// Include FASTQ config to prepare for a case when the entry point is 
+// FASTQ metadata CSV or FASTQ input directory
+includeConfig "${pd}${fs}conf${fs}fastq.config"
+
+if (params.pipeline != null) {
+    try {
+        includeConfig "${params.workflowsconf}${fs}${params.pipeline}.config"
+    } catch (Exception e) {
+        System.err.println('-'.multiply(params.linewidth) + "\n" +
+            "\033[0;31m${params.cfsanpipename} - ERROR\033[0m\n" +
+            '-'.multiply(params.linewidth) + "\n" + "\033[0;31mCould not load " +
+            "default pipeline configuration. Please provide a pipeline \n" +
+            "name using the --pipeline option.\n\033[0m" + '-'.multiply(params.linewidth) + "\n")
+        System.exit(1)
+    }
+}
+
+// Include modules' config last.
+includeConfig "${pd}${fs}conf${fs}logtheseparams.config"
+includeConfig "${pd}${fs}conf${fs}modules.config"
+
+// Nextflow runtime profiles
+conda.cacheDir = "${pd}${fs}kondagac_cache"
+singularity.cacheDir = "${pd}${fs}cingularitygac_cache"
+
+// Cleanup after running
+cleanup = true
+
+profiles {
+    includeConfig "${pd}${fs}conf${fs}computeinfra.config"
+}
\ No newline at end of file