--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/nextflow.config	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,162 @@
+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 = '/tmp'
+singularity.cacheDir = '/tmp'
+
+// Cleanup after running
+// cleanup = true
+
+profiles {
+    standard {
+        process.executor = 'local'
+        process.cpus = 1
+        params.enable_conda = false
+        params.enable_module = true
+        singularity.enabled = false
+        docker.enabled = false
+    }
+
+    stdkondagac {
+        process.executor = 'local'
+        process.cpus = 4
+        params.enable_conda = true
+        params.enable_module = false
+        singularity.enabled = false
+        docker.enabled = false
+    }
+
+    stdcingularitygac {
+        process.executor = 'local'
+        process.cpus = 4
+        params.enable_conda = false
+        params.enable_module = false
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+    }
+
+    raven {
+        process.executor = 'slurm'
+        process.queue = 'prod'
+        process.memory = '10GB'
+        process.cpus = 4
+        params.enable_conda = false
+        params.enable_module = true
+        singularity.enabled = false
+        docker.enabled = false
+        clusterOptions = '--signal B:USR2'
+    }
+
+    eprod {
+        process.executor = 'slurm'
+        process.queue = 'lowmem,midmem,bigmem'
+        process.memory = '10GB'
+        process.cpus = 4
+        params.enable_conda = false
+        params.enable_module = true
+        singularity.enabled = false
+        docker.enabled = false
+        clusterOptions = '--signal B:USR2'
+    }
+
+    eprodcingularity {
+        process.executor = 'slurm'
+        process.queue = 'lowmem,midmem,bigmem'
+        process.memory = '10GB'
+        process.cpus = 4
+        params.enable_conda = false
+        params.enable_module = false
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+        clusterOptions = '--signal B:USR2'
+    }
+
+    cingularity {
+        process.executor = 'slurm'
+        process.queue = 'prod'
+        process.memory = '10GB'
+        process.cpus = 4
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+        params.enable_conda = false
+        params.enable_module = false
+        clusterOptions = '--signal B:USR2'
+    }
+
+    cingularitygac {
+        process.executor = 'slurm'
+        executor.$slurm.exitReadTimeout = 120000
+        process.queue = 'centriflaken'
+        process.cpus = 4
+        singularity.enabled = true
+        singularity.autoMounts = true
+        docker.enabled = false
+        params.enable_conda = false
+        params.enable_module = false
+        clusterOptions = '-n 1 --signal B:USR2'
+    }
+
+    konda {
+        process.executor = 'slurm'
+        process.queue = 'prod'
+        process.memory = '10GB'
+        process.cpus = 4
+        singularity.enabled = false
+        docker.enabled = false
+        params.enable_conda = true
+        params.enable_module = false
+        clusterOptions = '--signal B:USR2'
+    }
+
+    kondagac {
+        process.executor = 'slurm'
+        executor.$slurm.exitReadTimeout = 120000
+        process.queue = 'centriflaken'
+        process.cpus = 4
+        singularity.enabled = false
+        docker.enabled = false
+        params.enable_conda = true
+        params.enable_module = false
+        clusterOptions = '-n 1 --signal B:USR2'
+    }
+
+    gxkubernetes {
+        process.executor = 'k8s'
+        k8s.namespace = 'galaxy'
+        k8s.serviceAccount = 'galaxy'
+        k8s.maxErrorRetry = 5
+        singularity.enabled = false
+        docker.enabled = true
+        params.enable_conda = false
+        params.enable_module = false
+    }
+}